Field forward sequencing in naval environments

Sophie Colston a microbiologist at the US Naval Research Laboratory opened by describing the diverse environments within which the US Navy operates, incorporating both offshore (including over 250 battle ships) and onshore installations such as hospitals, overseas medical research units, and emergent field laboratories. As the US Navy’s corporate laboratory, the US Naval Research Laboratory (NRL), undertakes a wide spectrum of research, including the utilisation of next-generation, high-throughput sequencing to analyse discreet microorganisms and microbial communities.

Recognising the potential value of rapid, on-site deployment of real-time sequencing, the team at NRL have utilised the MinION to develop a small, fully portable sequencing laboratory, enabling the investigation of microbial samples from diverse sources.

Sophie gave an overview of two pilot studies that are currently under way to assess the utility of this mobile sequencing lab. The first study described was designed to examine the microbial communities present on the interior surfaces of an operational naval vessel. The premise being that the interior surfaces would act as simple proxies for human microbiomes, potentially providing actionable insights into crew health swab samples were obtained from a number of washroom surfaces (including toilet seats, tap handles, and inner and outer door handles) from different locations within the vessel. Using a 16S targeted sequencing approach, the team were able to clearly identify the bacterial phyla present in each sample and their relative abundance. For full details on the microbes detected, Sophie referred the delegates to her poster. While in this initial study, just one sampling timepoint was used, the eventual objective is to sample at multiple critical timepoints during the vessel’s operational cycle to track changes to these microbial communities.

Another potential application of the mobile sequencing lab is the identification of biological threats. Sophie explained how the team at NRL are currently collaborating with the Biological Defense Research Directorate (BDRD) to develop a rapid workflow for field-based detection of biological threats within 6 hours of sample acquisition. For this work, they are utilising the MinION, Flongle, and MinIT. Sophie explained that in addition to targeted assays, the team are also working on unbiased metagenomic sequencing protocols, which would allow more comprehensive analysis and taxonomic classification of microbial samples.