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.