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DNA sequencing in microgravity on the International Space Station (ISS) using the MinION


Date: 29th August 2016

The portability, ease-of-use and low power requirements of Oxford Nanopore’s MinION enables sequencing in non-laboratory environments and even in microgravity!

Fig. 1 Astronaut Kate Rubins on the ISS

The first ever sequencing in space was performed on the ISS by Kate Rubins

The portability of the MinION allows users to sequence in non-laboratory situations. To demonstrate this, in collaboration with NASA, we tested the MinION aboard the ISS. The ISS orbits 400 km above the Earth, and travels at approximately 28,000 km/h and so is in constant freefall, with a continuous microgravity environment (Fig. 1). A mixture of lambda phage, mouse and E. coli DNA libraries was prepared on Earth and was sequenced on the ISS over four MinION runs. The same mixture of libraries was sequenced over four MinION runs on Earth, to act as a control. 

Fig.2 Analysis workflow showing read quality for runs a) on Earth b) on the ISS

Results from the first ever space sequencing done on MinION and R7.3 flow cells

We created a chained workflow consisting of 1D basecalling of raw fast5 files, 2D basecalling, extraction of quality scores and read-length information (Figs. 2a and 2b), and finally alignment. The workflow is capable of processing individual reads as soon as they are generated on the MinION, meaning that data can be analysed almost in real time. Due to internet limitations on the ISS, data was downloaded and processed immediately on Earth following completion of each run. In this way, basecalling and alignment of the data were performed almost simultaneously, allowing the success of the experiment to be confirmed shortly after the workflow was started.

Fig. 3 Percentage of reads mapping to each reference genome for Earth and ISS runs

Sequence data from ISS runs is indistinguishable from ground controls

For alignment, the workflow took 2D reads and used Minimap to establish whether each read mapped to E. coli K-12, lambda phage or mouse BALB/C genomes. Reads aligning to both lambda and E. coli genomes were resolved using BLAST to identify the correct placement. Any reads that could be resolved in this way were placed into the ‘Unknown’ group. Reads that did not align to any of the three reference genomes were placed into the ‘No_match’ group. Fig. 3  shows the percentage of reads assigned to these categories for three Earth and all four ISS runs together. Ground 2 was not included because the run was not successful. 

Fig. 4 Identification of bacterial genera found on Aquarius

NASA Extreme Environment Mission Operations (NEEMO) project

The NEEMO project involves performing scientific research in the Aquarius underwater laboratory, 5.6 km off the coast of Key Largo, Florida. The laboratory is 19 metres below the water surface, and the hostile environment is analogous to that found in space. We have been working with NASA to perform metagenomic surveys of various surfaces found on Aquarius. The approach involves DNA extraction, 16s PCR, and MinION sequencing to identify bacteria down to genus level (Fig. 4). In the future, similar surveys may be done on the ISS to monitor the astronauts’ environment, to check the cleanliness of the air and water, or to monitor changes in astronauts’ health by analysing their microbiomes or gene-expression levels. 

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