It was great to see Lauren Lui from the Lawrence Berkley National Laboratory present at London Calling 2024 on “An unprecedented metagenomic landscape of European and North American coastal samples.” Lui is a research scientist and, while at Miten Jain’s lab at Northeastern University, loaded 34 PromethION flow cells, generating 5 Tbases of data! Lui spoke about the San Francisco Estuary and its importance for human activities. The estuary has not experienced eutrophication. A hypothesis as to why this isn’t happening is that turbidity prevents algae from growing. In 2022, Lake Merritt had a harmful algal bloom that caused thousands of fish to die. Lui studies the microbiome because the microbes are important for element cycling, and nitrous oxide is a greenhouse gas. Lui spoke about the standards for MAGs that were developed for Illumina sequencing for the completeness of metagenome-assembled genomes (MAGs). For example, for one sample, they obtained 150 Gbases of metagenomic data. With Nanopore sequencing, better metagenome assemblies are possible. Lui partnered with the USGS to optimize the bioinformatics and DNA extraction from water filters. The extraction method increased the average size of fragments to 200+ kb. The new binning algorithm can help obtain more information at the strain level. Lui obtained algae, giant virus sequences, and more from these samples! Now they have ~5Tb of Nanopore Baltic Sea sequencing to compare to the estuary information! Lui has been a great KBase collaborator and contributor to bioinformatics tools and workflows.
