Metagenomics: Some Initial Reading
- Wei Xie
- Oct 2, 2022
- 2 min read
Metagenomics is a promising field that has contributed vital new knowledge of the microbial worlds in the world, from our guts to ocean trenches. In a nutshell, it is the extraction and analysis of "environmental DNA"(eDNA), DNA extracted from an entire sample collected from the environment.
Unlike traditional DNA extraction, this requires more involved computational analysis since an eDNA sample may contain DNA fragments from multiple different species that live in the same environmental source collected from.
Value
In addition to interesting ecological and evolutionary insights, the discoveries yielded through metagenomics have given us humans new, more efficient pathways to produce life-saving natural pharmaceutical compounds, and to subdue the toxicity of some of our pollution as in the field of environmental biotechnology, just to name a few.
In browsing interesting episodes on biotechnology and bioinformatics for beginners like me, I came across Leo Elworth's interviews with Matthew Schechter, an introduction to metagenomics perfectly toned-down enough for me to follow, while providing a comprehensive overview of the motivations, applications, value and current main methods in the field.
All About Piecing Together DNA
Central to genomics and always the first step in analyzing genetic data is piecing together the initial DNA fragments, or reads, into a complete continuous sequence that is hopefully identical to the true genome (directing every cell of the organism) that the fragments constituted.
Now, the equivalent in metagenomics would currently be the holy grail--piecing the eDNA reads into a complete genome for every organism represented in the sample. Thus, all the methods discussed in Part I of the interview pertain to this challenge, and I began exploring tetranucleotide analysis and differential coverage further on the interwebs.
With the substantial help of (Tetra-Nucleotide Analysis (TNA) – EzBioCloud Help Center, n.d.) and the original paper that brought differential coverage into the field, (Albertsen et al., 2013), the following notes summarize some initial readings of mine on metagenomics. I hope this article may be of value to anyone else interested in learning about metagenomics.
References
Tetra-Nucleotide Analysis (TNA) – EzBioCloud Help center. (n.d.). Retrieved 2 October 2022, from https://help.ezbiocloud.net/tetra-nucleotide-analysis-tna/
Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K. L., Tyson, G. W., & Nielsen, P. H. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology, 31(6), Article 6. https://doi.org/10.1038/nbt.2579
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