Dylan Maghini from Stanford University presented at the Nanopore Community Meeting 2019 on “Genomes from metagenomes: assembling bacterial genomes with nanopore sequencing.” Maghini spoke about the importance of the human gut microbiome on human health. They noted that we still have an incomplete understanding of the gut microbiome. For example, de novo assembly aims to build microbial genomes from stool DNA. The metagenome-assembled genomes (MAGs) are often fragmented if generated with short reads, especially within and across repetitive elements. Bins can be incomplete or contaminated by sequences from other organisms. Maghini and the team wanted to develop an extraction and computational protocol for stool samples. Eli Moss used a DNA extraction protocol using a variety of enzymes and SPRI beads. This procedure helped obtain longer DNA. The sequences were then curated and assembled. Nanopore sequencing of a mock community was able to circularize genomes. Sequencing of human stool was able to close several bacterial genomes. One example was Prevotella copri, which is highly abundant. The team noticed that there are numerous insertion sequences across the P. copri genome. Interestingly, Maghini noticed that the insertion sequence abundance varies across the genome and over time. Insertion sequences were adjacent to nutrient utilization, biofilm, and antimicrobial resistance genes. Another closed genome was a putative Cibiobacter. Phage and insertion sequences were also abundant in this genome. Having a closed genome was instrumental in better understanding and classifying this genome. Maghini also shared data from new organisms in South Africa. One limitation of this approach is that some “highly abundant organisms still evade circularization.” Maghini explained that they think that longer reads will help classify these organisms. They found an interesting inverse correlation between the number of genomes in a genus and circularization. I enjoyed this session as it visually demonstrated the power of long reads in circularizing genomes from metagenome assemblies.
