Interview: Digging up the dirt using rapid genomic discovery with nanopore sequencing

Technology Networks webinar

Date: Thursday 27th June 2019

Time: 11am EDT/4pm BST/7am Alaska

Speaker: Devin Drown, Assistant Professor at University Alaska Fairbanks

Devin Drown is Assistant Professor at the Institute of Arctic Biology, and Department of Biology and Wildlife at the University of Alaska Fairbanks. His research uses a combination of genomics tools, greenhouse and field studies, along with mathematical modelling to understand coevolutionary interactions. He also engages undergraduate researchers in measuring and testing the effects of the Alaska soil microbiome on ecosystem health, seeking to understand how these plant-microbe interactions may influence how the plant community responds to changing climatic conditions. We caught up with Devin to talk about his research in Alaska, how he became interested in genomics and his experience using VolTRAX in his work.

What are your current research interests?

My lab’s research broadly addresses coevolutionary interactions using a combination of molecular analysis and mathematical modelling in both field and controlled laboratory settings. Our work seeks to understand how permafrost thaw decreases environmental health in boreal and arctic regions - our central hypothesis is that permafrost thaw changes the microbial environmental reservoir of northern soils in a way that negatively affects environmental health and human populations. One key aspect of this research is to understand how environmental change is affecting antimicrobial resistance, as well as to understand plant-microbe interactions in this changing environment.

What first ignited your interest in metagenomics?

I can honestly say that the original MinION early access program drew me deep into genomics in general, as once our lab started collecting data sets right on our own bench, I was hooked. My lab had been comfortable using 16S for community analysis, but the field has been moving in the direction of using metagenomic data for a while.

Can you tell us more about how long-read sequencing technology is changing your field?

In my field being able to generate assembly free, gene length reads pushes the boundaries of metagenomics. Each read that we collect from our samples, whether soil core or river water, has the potential to tell us something new about what’s happening in that sample. We started to use nanopore sequencing to investigate antibiotic resistance and, while we started with phenotypic screens for resistance, here the technology has enabled us to detect genes potentially responsible.

What are your initial impressions of VolTRAX and how can you see it impacting your work?

I think the VolTRAX has great potential and my overall reaction of the V2 device continues to be positive. Running through the protocol is straightforward - the number of ports has increased and with multiplexing, there will be as many as 25 loadings. The active feedback makes sure that you are loading each reagent into the correct port. As an added bonus, the automation of the device was quite ideal for my schedule. I was able to quickly load all of the required reagents, then ran to a 1-hour meeting. I returned to find my library complete and ready to extract, so I loaded this on a waiting flow cell and was off to another meeting.

Right now we’ve used it in just a couple of limited projects, but it is always of interest to new students and it’s one of those technologies that inspires students to ask a lot of questions, as they want to know what else they can do. I also have a project with Dr Eric Bortz investigating African Swine Fever Virus in Ukraine – our focus at the moment is basic genomics, but as are working with a diagnostic lab, I’m always thinking about how we might standardize the screening process in the future. For me, the VolTRAX fits in that part of the process.

What is your advice for someone getting started?

For someone just getting started heading up a lab, my advice is to stay flexible. I started my position with several project outlines, but some of my more successful projects were ones that came about because I was open to new ideas. My advice for someone just getting started with long-read nanopore sequencing is to listen and ask questions of the Nanopore Community. The technology has changed so much in the past 3 years and continues to rapidly advance and so techniques and methods can often get out of date - but there are a lot of wonderfully helpful people in the Nanopore Community and I’ve certainly benefitted from their continuous help.

What’s next?

We’re looking to expand our Alaskan experiments as so far, we have focused a great deal of our efforts on a couple of very local field sites where we have access and we have a couple of projects that seek to expand this. While a lot is unknown about the Alaskan soil resistome, we now have some baseline data that we’ve started to combine with our phenotypic screens. This should help us start building a better understanding of the environmental reservoir of resistance.

Register for Devin's webinar here.