The Meta in Metagenomics
In the subfield of Biology called genetics a discipline has emerged. It is called Metagenomics. I use the term discipline specifically because if you are doing metagenomics research you are a cross-disciplinary jack of all trades researcher and everyone wants you, cause you can make sense of the maelstorm they call their data and you have the ability to design, create, and run a data experiment that makes sense of some vagary brewing in the crook pot of a professor’s brain.
Some imagery might help, picture a fungus, specifically a fungus pushing its fruit out of the ground, and then exploding, spreading its spores far and wide. Prior to the advent of modern computational capabilities, geneticists studied simple questions focused on a single gene, often in an organism easy to culture. Then two things happened; one is we got bigger, badder, and cheaper computers. Two, we found a way to inexpensively sequence hard drive loads of DNA. Suddenly geneticists were producing prodigious amounts of data and they needed someone to do something with it. Bioinformaticians and Biostatisticians finally had a home. But no field of biology breeds them quite as vigorously or intensely as Metagenomics. Which is why it’s called METAgenomics. It is much more badass than genetics or even the glamorous epigenetics.
Meta: According to the most reputable source, wikipedia, “Meta is a Greek preposition and prefix meaning after or beyond” and in the bastard child of a language we call english, it’s used to mean a concept that is an abstraction from another concept. So says the urban dictionary. In genetics, it is referring to DNA that is not taken directly from a specific organism, but rather it is taken from a population within a ecosystem, also called eDNA or environmental DNA. It is not one species you are sampling, but organism from across all domains of life. Sounds impressive right? Trust me, it is much more impressive than you think.
Lets add some numbers to really put things into context. The smallest sorta life like thing is a virus. Viruses have anywhere from a hundred thousand to two million base pairs. Up the size a bit to bacteria and you are looking at up to fourteen million base pairs. But what about eukaryotes? Basically everything not bacteria. Well, on the small single cell end of things we are looking at 10 million base pairs and up. Start stacking cells and suddenly genomes get big. Big as in the model organism, C. elegans, a worm with 100 million base pairs and that’s on the small end. Human cells have 3.6 billion base pairs to deal with. Which comes out to be roughly 3.6 gigabytes of data. It is easy to imagine how unwieldy that much data can be. What happens when you want to start comparing genomes of multiple species or even of the same species? It’s god awful if not impossible and also why comparative geneticists are crazy and good scientists don’t talk to them.
Enter Metagenomics: These badass scientists are also crazy. In fact, you could say they are even more insane than comparative geneticitists. Instead of taking one organism and comparing its genome against another, they like to take hundreds if not thousands of genomes, stick them in a blender, stick it on the smoothie setting, then take the resulting mush and sift through it using a strainer made of complicated mathematics and unreadable algorithms. The end products are beautiful graphs and statistics describing worlds science would never get to see if scientists only studied organisms in the lab.
It is difficult to do this smoothie trick with large, multicellular organisms. But it works great for things like bacteria, viruses, and any other microbe out there. This is good, because the majority of microbes out in the wild will never see the sterile environment of the lab; because they are picky. They need special conditions to thrive and when there are millions of different species all being picky, the lab scientists choose the good, easy going, species. Which is wonderful for doing research into the fundamental nature of genetics, but when you want to understand what’s happening out in the real world you need to be able to look at what’s actually living in the real world.
Metagenomic scientists are like the astronomers looking out into the edges of the universe for new planets and galaxies. But their universe ranges from the gut of a person to the vast oceans covering our planet. The things they have discovered tell a story of a world in which humanity is deep in a relationship with microbes, a relationship we have been approaching all wrong. Our immune system is constantly chatting with the bacteria in our intestines, letting each other know who’s good, bad, and ugly. Scientists have found unknown bacteria in toxic mine waste breaking down the toxic stuff we left there. In agriculture, researchers have been able to identify what microbe is causing a disease and are also able to see the incredible diversity of microbes in the soil, even identifying fungi important to the health of crops. New compounds important to the creation of medicines or biofuels have been found using metagenomic analysis of eDNA. The list continues and is growing everyday.
The more we discover using metagenomic analysis the more we realize that when we dump loads of fertilizers, pesticides, herbicides, fungicides, and other nasty chemicals onto our crops to “help them grow” we are actually killing the microbes which actually help them grow. Or when we leave toxic compounds strewn across the landscape such as with mining and oil operations, it is the microbes which clean up after us. When we use antibiotics we kill all the bacteria in our gut, the same bacteria that helps us digest our food, prevent nasty infections, and produce certain compounds we need to stay healthy. It becomes even more incredible when we consider that phytoplankton, sunlight eating microbes of the ocean, are responsible for the majority of the oxygen we breathe and the removal of carbon dioxide from the air. They are also the base of the food chain, without phytoplankton there would be no tasty fish, crabs, or oysters for us to eat. Global warming is causing the ocean to become more acidic, changing what phytoplankton thrive and with it the what animals further up the food chain thrive.
The profound impact that metagenomics is having on our understanding of the world is brewing a new generation of scientists who, while legally insane and treated like a highly sought after commodity, are also some of the most ridiculously amazing scientists out there.
