MinION Below Zero: sequencing microbes and marine mammals, birds, and the Alaskan coastal environment from low-quality samples, including whale snot

Eric Bortz

Eric Bortz, University of Alaska Anchorage, USA


The waters of Alaska harbor a diverse wildlife and microbial ecology under intense pressure from human activity and changing climate. We applied random hexamer REPLI-g amplification and nanopore sequencing (LSK109 MinION) to analyze opportunistic cDNA samples: seabird and marine mammal surveys, and whale blow captured using drone technology (‘snotbots’). Kraken2 taxonomic classification identified avian influenza in northern fulmars from the Bering Sea. We also found influenza of avian origin in stranded ringed seals and Stejneger’s beaked whale. Respiratory vapor collected from humpback whales off Stellwagen Bank, Alaska, identified gram-negative aerobes and eukaryotes, highlighting the vast microbial reservoir in Alaskan waters.


Eric Bortz currently works in the Department of Biological Sciences, University of Alaska Anchorage. Eric’s specialty is research in genomics of emerging viruses. His lab applies nanopore sequencing methods to understand avian influenza, SARS-CoV-2, African swine fever, and other pathogens that impact human, animal, and environmental health.