‘Omics, tools of the trade.

My tragic backstory™ – I was a computer science major but found way more enjoyment in the prospects of research than crunching code all day; I’m also a way better project manager than software dev.  Bioinformatics is a solid left-field change that’s taken my background in biology and smashed it with computer science foundations I’ve built. Now I’m participating in a two-year program with the NIH focusing on health informatics, but with an emphasis on bioinformatics, and the microbiome of the lungs… and I love it.

With studying the microbiome/biota, how do we rip out the data we need? What do we even need and what are we looking for? ‘Omics technologies provide the basis for understanding microbiomes, and there are four general areas that answer different types of questions:

·         Genomics – What are the microbes and their genes in the sample?

·         Transcriptomics – Which genes are actually being used?

·         Proteomics – What proteins are being made?

·         Metabolomics – What are the metabolites/end products?

A little housekeeping before diving in – all of the ‘omics tech uses sequencing, so first we have to understand what that means and how we get there. There are a few key steps (Extraction -> Polymerase Chain Reaction -> Sequencing). To extract we take a sample, lyse the cells with detergents, destroy/purify the sample with enzymes, then after centrifuging the sample we can take it into a clean tube. PCR uses primers to copy a specific section of DNA we want to sequence, then uses hot and cold cycles to multiply the DNA. These are done in a wet lab.

Finally, sequencing is done through high-throughput sequencing robots (or God-forbid by hand). Now we have our data.

Photo by Devin Lyster on Unsplash

What does each technique give us? Genomics sequencing looks at the DNA, it shows us which bacteria is present and what genes they have. There are a few methods actively used. 16S rRNA (ribosomal RNA), is useful in identifying bacteria and archaea based on that ribosomal RNA sequence. We also have whole-genome shotgun sequencing (the coolest technique name in all of science), to look at all genes. Both of these can be used in metagenomics — meta = all the microbes in a sample not just one. There are also ways to sequence an individual bacterial genomic sequence.

Transcriptomics looks at the messenger RNA to see which genes are being expressed. The data it provides is a more observant look at which genes are being used in the sample. Proteomics looks at the protein functions bacteria are actively taking part in, narrowing down which amino acids from the RNA are being translated into proteins. As we know, proteins are the workforce of the cell; acting as messengers, moving stuff around, and kickstarting chemical reactions. Lastly, data on the end products (hormones, sugars, etc.), falls under metabolomics.

If the microbiome interests you, learn more about it here. It’s where I’m getting all this useful info, i.e. here’s my citation.