Three oral cavity datasets are available in curatedMetagenomicData:

## [1] "BritoIL_2016 (PMID: 27409808)"       
## [2] "Castro-NallarE_2015 (PMID: 26336637)"
## [3] "HMP_2012 (PMID: 22699609)"

This heatmap shows presence/absence of genera and species in the Papillomaviridae family of viruses, for individuals where Papillomaviridae is present with at least 0.1% relative abundance. Alphapapillomavirus_1 is the most common species.

The maximum absolute correlation between the clades of the above heatmap with more than two non-zero observations and any non-viral relative abundance is:

##                          s__Neisseria_macacae
## s__Alphapapillomavirus_1                 0.32

This correlation is highly significant, by Pearson’s test or Wilcoxon rank-sum test:

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  hpvmat2[rownames(getDimMax(cormat)), ] and othermat[colnames(getDimMax(cormat)), ]
## W = 92693, p-value < 2.2e-16
## alternative hypothesis: true location shift is not equal to 0

Viewed as a boxplot:

HMP subsites

Conclusion

The presence of Alphapapillomavirus_1 species in the oral cavity is correlated with increased abundance of Neisseria macacae. Sample size is too small to identify potential associations with other members of the Papillomaviridae family.