The hidden diversity of archaea and bacteria in the human microbiome : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Microbiology at Massey University, Manawatū, New Zealand
Current methods of metagenomic analysis require deep sequencing to identify microorganisms that are present at low abundance in complex microbiomes, including the human gut microbiome. The few known archaeal taxa present in the human gut are low in abundance in comparison to bacteria. This raises the question about whether the full diversity of human gut-associated archaea is known. To increase the resolution of metagenomic analysis, a new DNA normalization technique utilizing duplex specific nuclease (DSN) was used to enrich for DNA from “rare” archaeal and bacterial taxa isolated from two human metagenomic faecal samples. This DSN based normalization method failed to enrich for archaeal DNA, as it was digested by the DSN, however, it succeeded in enriching for low abundance bacterial DNA. This indicated that further optimization of the normalization method is required to enrich for low abundance archaeal DNA in human metagenomic samples. Whole metagenome shotgun sequencing was also used to identify a microbial community composition of participants gut microbiota including archaea. WGS identified a higher than anticipated diversity of archaeal taxa in gut microbiomes from both participants. Regardless of higher diversity, the low abundance of archaea in the human gut still render them as a part of rare biosphere. We envisage that with further optimization of DSN-based normalization, enrichment of “rare” taxa will improve detection resolution and therefore enhance our current understanding of the diversity of both archaeal and bacterial species in human gut microbiome.