Research with impact at ASM Microbe

Even the smallest of organisms can have a big impact.

At the American Society for Microbiology (ASM) Microbe congress 2024, scientists, researchers, and healthcare professionals gathered to explore how the latest microbial research is shaping the future of humanity.

From ecology and environmental sciences to clinical research and public health, read on to find out how highly accurate, any-length nanopore reads are enabling groundbreaking discoveries in the microbial world.

No compromises: Assembling complete, highly accurate bacterial genomes

A highlight was Ryan Wick’s (University of Melbourne, Australia) presentation on bacterial isolate genome assembly tools and strategies, demonstrating the latest basecalling accuracy of nanopore sequencing and a gradual shift from multi-platform assemblies to using nanopore sequencing alone. He presented an assembly of Klebsiella which was 99.99995% accurate (Q63.0) with just nanopore data – no short-reads required! This is an incredible feat, and opens the door to nanopore-only assemblies becoming the standard practice for microbiology research.

At ASM, the impact of nanopore sequencing was seen beyond bacterial studies. Corina L. Tabron et al. (American Type Culture Collection, US) investigated whether nanopore sequencing could improve the quality of viral genome assemblies compared to short-read sequencing. Nanopore sequencing was found to considerably improve the average assembly length and genome completeness, and drastically reduced the contig counts.

In the realm of metagenomics, Anna Cusco (Fudan University, China) found nanopore-only sequencing was suitable for the construction of highly contiguous metagenome-assembled genomes (MAGs), with 43% of the MAGs being high-quality single-contig assemblies.

A busy booth at ASM Microbe 2024 with lots of people milling around with a large nanopore banner overhead

Greater capacity to identify species

As well as providing a complete picture of the genetics of an individual organism, researchers were also sharing how they use nanopore sequencing to provide comprehensive insights into the microbiome. Taylor E. Gin et al. (North Carolina State University, US) shared how nanopore sequencing detected significantly more species-level taxa than short-read approaches when using a 16S targeted approach. This provided a more holistic understanding of flea microbiomes, aiding prognosis and treatment of infected pets.

With the knowledge that nanopore sequencing provides a complete and accurate picture, researchers are confident taking these devices into the field. Kiaqin Bian (Georgia Institute of Technology, US) discussed her nanopore workflow for identifying and quantifying microorganisms on site. With results comparable to those produced using short-read sequencing, the benefits of portability come to the fore.

On  stage there is a man to the left, standing behind a podium looking at the 4 speakers sat to their right. One of the speakers has a mic and the others are listening to her talk.

Accuracy in the field

Portability allows researchers to effectively undertake surveillance programs on infectious diseases and respond in an outbreak scenario. Matthew Keller (Centers for Disease Control and Prevention, US) and Josh Quick (University of Birmingham, UK) discussed their work, showcasing how they are using nanopore sequencing to help improve human health.

Want to learn more? Click the link to find out how nanopore sequencing can support your microbiology research.