C-section, the mother’s skin or the environment. The fact that the microbiome is acquired anew each generation is in stark contrast to the human genome, which is inherited.6

A second universal property is that each adult body part has a distinct microbial community composition. HMP 16S rRNA data reveal a clustering of certain microbial taxa with particular body sites, such as the skin, gut, oral cavity, airways, or urogenital tract, regardless of host gender, age, weight, or any other host metric. Costello et al. (2009) reported a similar finding—that microbial community composition is dictated by body site. Proctor observed that body site clustering is probably driven by the same types of factors that drive microbial colonization and growth in other environments (i.e., pH, temperature, condition of the substrate, other ecological parameters). She said, “The human microbiome is probably like a lot of other microbial ecosystems out there on the planet.”

However, while 16S rRNA data show that microbial composition varies among body sites and even within body sites between individuals, metagenomic data indicate that the major microbial metabolic pathways are effectively the same across body sites. So even though each body site has its own unique microbial assemblage, all of those assemblages, regardless of composition, appear to function similarly with respect to metabolism. This is true for healthy individuals in the HMP study, but it remains to be seen how microbial metabolism compares between healthy and diseased individuals.

A final universal property of the human microbiome is that the gut microbiome changes over a lifetime, with microbiomes in elderly people (aged 65 and over) being very different from microbiomes in middle-aged adults. As part of the ELDERMET project,7 Claesson et al. (2011) reported a greater proportion of Bacteroidetes, more overall microbial taxonomic diversity, and greater individual variation in microbial taxonomic composition among elderly compared to middle-aged individuals. With babies, microbial succession during the first 1 to 2 years of life begins to vary with the transition to a more diverse diet (Yatsunenko et al., 2012), as opposed to the relative stability seen with breast-fed infants. Eventually, by the second year of life, the taxonomic composition of the gut microbiome stabilizes, and the gut develops what appears to be an adult microbiome (Palmer et al., 2007).

On the basis of HMP studies, Proctor noted that evidence to date does not support the notion of a core microbiome, at least not at the species level; the concept of enterotypes; or the classification of microbiomes of

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6 See the summary of Josef Neu’s presentation in Chapter 3 for a discussion of microbiota acquired prior to birth, during the third trimester of pregnancy.

7 Funded through the government of Ireland, ELDERMET is a study of diet, gut bacteria, and health status in elderly (65 years and older) Irish subjects.



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