12 December 2017

Science for Life

Discovering new (microscopic) life forms

Bastiaan von Meyenfeldt

Archeologists and paleontologists study human and animal history through fossils, ruins and artefacts. I too, have always harbored a fascination for deep time (geologic time) and science, especially when we’re talking about things on the edge of what we know. Unfortunately, I’m too impatient to sift through dirt with a brush, which is why I’ve merged my interests in evolution with high tech. 

I’m a bioinformatician and theoretical biologist - I use computers to study biology, and for those budding bioinformaticians out there, it’s not just about sitting behind a computer all day. What if I told you that because of this broad field, I’ve been to Duke University to study hydrothermal vents, frozen my fingers while removing ice core samples at the north pole (and carried a firearm against polar bears!), and been on a boat for a month in the North Atlantic collecting water samples?

All of this guided me to metagenomics and microbes, microscopic organisms such as bacteria and viruses. All life on Earth is touched by microbes, from our gut microbiome to agriculture to the ocean systems, and they live in almost every habitat, including some of the most extreme environments that we know of.

A holistic search

Up until recently, we’ve studied microbes one by one, cultured under an artificial environment in the lab, outside of their natural habitat. With metagenomics, we sequence the DNA in a sample of an environment, everything in a water drop or a spoonful of soil. Think of it as a holistic search for general patterns in biology. This means that we can discover rare microbes that we can’t culture in the lab and capture the diversity of existing and novel microbes. This also gives us a glimpse into the molecular dynamics of these communities and our biosphere.

I’ve been to Duke University to study hydrothermal vents, frozen my fingers while removing ice core samples at the north pole, and been on a boat for a month in the North Atlantic collecting water samples

When we sequence the metagenome, we get massive amounts of data in the form of short pieces of DNA, called short reads. Traditionally, these are aligned to a reference database in order to construct the genomes present in the sample. For genomes that have never been seen before, we have no reference database, so we have to be creative. We can de novo assemble the short reads - a bit like gluing together reads that have some overlap – and then cluster the resulting longer DNA sequences (called scaffolds) that we suspect are related into groups. This clustering, or binning, is done without references but by using features extracted from the sequences themselves. We do this with existing computational algorithms and strategies when possible, but when we don’t have a tool, we write code to make new ones, for example, new types of computer searches and computational models to understand the data.

Metagenomics is widely applicable

The field of metagenomics is quickly growing and is providing us with a deeper understanding of microbes, not only in human health or potentially global applications (for example, producing biofilms to clean up oil spills), but also in our everyday life, in waste treatment, detergents and food production. We can sample the human gut microbiome and study microbial diversity and function between people and its relationship to disease; identify new microbial genetic pathways and antibiotic resistance; and understand host-microbe interaction. Another example are biofuels, which are generated by the chemical conversion of plant material into ethanol. This is done by microbes and understanding these microbial communities will improve efficiency and the ability to scale-up production.

Acquired or ancestral?  

I study microbes via metagenomes from an ecological and evolutionary perspective, the timescales of which are very much interconnected for the microbial world. My personal passion is purely scientific – simply trying to understand. I’m really interested in exploring how microbes interact with each other and why certain types live together in order to populate the tree of life. The discovery of new species is always amazing, but what’s even more fascinating is figuring out whether their genome content is due to recent adaptation to an environment or due to really deep evolutionary ancestral branching. Who knows, maybe in the near future we can go into any environment, sequence the metagenome, and truly understand why we find the microbes living there, even though we have never had a glimpse of some of them before. 

Bastiaan von Meyenfeldt, PhD Candidate
Copromotor: Bas Dutilh
Promotors: Berend Snel, Paulien Hogeweg
Theoretical Biology & Bioinformatics
Utrecht University