Searching for Archaea: Why Metagenomics Could be Key

The near-universal presence of microbes in the environment is illustrated by their endless applications, from foods to perfumes and fuels. However, as the research community has learned, most the microbial universe, about 99 percent, cannot be cultured and studied in a laboratory. This has made it difficult to get a comprehensive grasp of each of the domains of life – bacteria, eukarya, and archaea. However, thanks to advances in genetic sequencing technology, researchers can now take advantage of whole genome sequencing (WGS) and metagenomics, or the study of microbes in their natural environments. As a study published recently in ­mSphere illustrates, metagenomics will be crucial to avoiding some of the pitfalls of processes like 16S rRNA sequencing.


In the mSphere publication, researchers show that the commonly used 16S rRNA sequencing technique overlooked about 90 percent of the diversity in archaea living in human and other great ape species’ gut microbiomes. Archaea are the microorganisms that represent one of the three domains of life (bacteria, eukarya, and archaea). Like bacteria, archaea are microscopic and single-celled, however they have a separate evolutionary history and biochemistry. Given that little is known about archaea, these researchers were hungry for information, and launched their study like most scientists looking for microbial diversity do – sequencing the 16S rRNA genes present in biological samples they collected.


In this case, the researchers collected various human and other great ape stool samples and used primers for the 16S rRNA sequencing known as “universal primers.” These primers are supposed to identify both bacteria and archaea present in samples. But when the researchers followed up their first round of sequencing with sequencing that used primers that were designed specifically to identify archaea, they found that the universal primers had neglected to identify a startling number of archaea. For instance, in human samples, the archaea-specific primer found 37 types of archaea whereas the universal primer had found one. The disparity only grew as the sequence data from the other great ape species were compared.


This type of oversight helps explain why microbiology has been moving towards more powerful sequencing techniques, like metagenomics. With metagenomics, a researcher can sequence all the genetic material in a sample, not just the 16S rRNA genetic information. That’s why many microbiome studies, especially smaller ones, have already begun using metagenomics. As this study indicates, further research is needed to better understand the roles archaea play in the gut microbiome, and metagenomics can help deliver that progress.