A lab in the field: applications of real-time, in situ metagenomic sequencing

Abstract

High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely-used second generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.

Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review

“…Due to its long sequence read length, MioION provides a better phylogenetic resolution, which is a key metric for species-level identification and provides the ability to delineate species [ 172 ]. Worldwide, MinION nanopore technologies were found to be effective in delivering further insights and real-time analysis for a broad range of applications, such as epidemiological surveillance, microbiome identification, and field diagnostics [ 173 , 174 ]. In plant viral diagnosis, this technique can provide an effective and rapid method for the detection and identification of the causative agent of the disease.…”

“…Currently, Oxford Nanopore MinION has proven to be effective for real-time analyses with an average sequence length of more than 15 kb [ 168 ]. MinION has been used to detect and determine the whole genome sequences of a range of animal and human viruses, including the ebola33, dengue34, zika35, influenza31, cowpox36, and Ross River viruses; however, its use for plant viruses is still in the preliminary stages [ 173 , 174 , 175 , 176 , 177 ]. A few of the related studies have presented promising results using MinION nanopore sequencing.…”

A Round Trip to the Desert: In situ Nanopore Sequencing Informs Targeted Bioprospecting

“…Our results demonstrate that DNA analyses can be integrated into the sampling roadmap, while keeping the duration of the journey under 72 h (Figure 1). The obtained sequencing yield was substantially higher than the output reported in other onsite studies (Latorre-Pérez et al, 2021), and it was comparable to the yield of runs performed on fully equipped laboratories (Nygaard et al, 2020;Urban et al, 2021). It must be noted that instead of directly sequencing in the field, we decided to set up a mobile laboratory 15 km away from the sampling location in an apartment with internet and electricity access.…”

“…Nevertheless, this technology is time-consuming and usually requires shipping the samples to a centralized sequencing facility. Therefore, in situ third-generation sequencing (TGS) strategies emerge as a promising alternative to this traditional approach ( Latorre-Pérez et al, 2021 ).…”

“…Among TGS technologies, the Oxford Nanopore Technologies (ONT) MinION system is especially relevant for in situ sequencing as it is the smallest sequencing device currently available, it is inexpensive in comparison to other TGS devices, and the obtention of long reads can be assessed in real-time ( Latorre-Pérez et al, 2021 ). Thus, sequencing data can be directly analyzed through bioinformatic pipelines that can be run on servers, laptops, or even mobile phones ( Mitsuhashi et al, 2017 ; Palatnick et al, 2021 ).…”