Degree of balancing selection predicts relative abundances of
bacterial species in the human gut.
The maintenance by balancing selection of genetic variation in
functionally important genes, such as multidrug efflux pumps, in
bacterial species may provide a competitive advantage to these species
in the human gut microbiome. To test the ecological consequences of
balancing selection for gut bacterial species, we asked whether the
relative abundance of bacterial species in the human gut microbiome was
associated with the degree of balancing selection evident in the genomes
of that species. For this analysis, the relative abundances of all SGBs
in the Human Microbiome Project (HMP) metagenomes sequenced from the
healthy human subjects cohort (Huttenhower et al., 2012) were estimated
using CoverM (https://github.com/wwood/CoverM). We then tested for
an association of species’ relative abundance estimates with the
species’ genome-wide Tajima’s D values as well as with the species’
maximum CORF Tajima’s D value. Species’ relative abundances were not
associated with genome-wide Tajima’s D (p -value >
0.05), but they were significantly positively associated with the
species’ maximum CORF Tajima’s D value (Figure 3A). Similarly, PGLS
indicated that the association between species’ relative abundance and
the species’ maximum CORF Tajima’s D value was also evident after
controlling for bacterial phylogenetic history (Figure 3B). These
analyses showed that the bacterial species containing CORFs with the
highest Tajima’s D values also displayed the highest relative abundances
in the human gut microbiome.