  Two species with similar resource requirements respond in a characteristic
way to variations in their habitat -- their abundances rise and fall in
concert. We use this idea to learn how bacterial populations in the microbiota
respond to habitat conditions that vary from person-to-person across the human
population. Our mathematical framework shows that habitat fluctuations are
sufficient for explaining intra-bodysite correlations in relative species
abundances from the Human Microbiome Project. We explicitly show that the
relative abundances of phylogenetically related species are positively
correlated and can be predicted from taxonomic relationships. We identify a
small set of functional pathways related to metabolism and maintenance of the
cell wall that form the basis of a common resource sharing niche space of the
human microbiota.
