Human surfaces and cavities are populated by numerous microbial communities, including bacteria, viruses, archaea, and fungi, which form a complex interactive network between themselves and the host. These inter-kingdom interactions are the result of millions of years of co-evolution, and are an intrinsic part of host health and disease balance. For example, intestinal bacterial communities have been associated with pathologic conditions such as inflammatory bowel diseases, colorectal cancer, obesity, and liver cirrhosis by 16S rRNA gene or whole genome metagenomic sequencing analysis.