Metagenomics is a very broad field that can often be summarized down to the analysis of a microbiome. These microbiomes are all around and inside us. They’re in the air we breathe, the water we drink and the food we eat. They’re high up in the atmosphere, at the bottom of the ocean, in pools of boiling acid - they exist everywhere that hasn’t been carefully sterilized. These microbiomes represent diverse ecosystems with countless species of prokaryotes, fungi, viruses, protozoa, plants, and more. The main challenges when studying them are how to isolate an individual species for study, and perhaps now more importantly, how can we possibly investigate all the complex interactions between them.
Microeukaryotes play important roles in diverse ecosystems, such as waterways, and can be incredibly difficult to culture in a lab. Fortunately, studies investigating them can employ a sequencing approach that only requires sample extraction and amplification5. Finally, the ITS region within fungal species is of clinical importance for microbiome analysis. It represents a region similar enough to capture most fungal species, but different enough that individual species can be told apart6.
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9Kong, Heidi H., and Julia A. Segre. "The molecular revolution in cutaneous biology: investigating the skin microbiome." Journal of Investigative Dermatology 137.5 (2017): e119-e122.
10Schöler, Anne, et al. "Analysis of soil microbial communities based on amplicon sequencing of marker genes." (2017): 485-489.
11Lundberg, Derek S., et al. "Defining the core Arabidopsis thaliana root microbiome." Nature 488.7409 (2012): 86.
12Gopal, Murali, and Alka Gupta. "Microbiome selection could spur next-generation plant breeding strategies." Frontiers in microbiology 7 (2016): 1971.