In situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day

Abstract

We present here a complete system for metagenomic analysis that allows performing the sequencing and analysis of a medium‐size metagenome in less than one day. This unprecedented development was possible due to the conjunction of state‐of‐the‐art experimental and computational advances: a portable laboratory suitable for DNA extraction and sequencing with nanopore technology; the powerful metagenomic analysis pipeline SqueezeMeta, capable to provide a complete analysis in a few hours and using scarce computational resources; and tools for the automatic inspection of the results via a graphical user interface, that can be coupled to a web server to allow remote visualization of data (SQMtools and SQMxplore). We have tested the feasibility of our approach in the sequencing of the microbiota associated to volcanic rocks in La Palma, Canary Islands. Also, we did a two‐day sampling campaign of marine waters in which the results obtained on the first day guided the experimental design of the second day. We demonstrate that it is possible to generate metagenomic information in less than one day, making it feasible to obtain taxonomic and functional profiles fast and efficiently, even in field conditions. This capacity can be used in the further to perform real‐time functional and taxonomic monitoring of microbial communities in remote areas.

Future Perspectives on the Application of the Oxford Nanopore® MinION™ Sequencer in Cultural Heritage Biodeterioration Studies

“…Due to the sequencer portability, handling features, adaptability and its analysis speed, the platform allows for an on-site analysis. In fact, multiple reports of such applications are currently available and the technique has been applied for real-time sequencing in differential environmental contexts, such as Ebola surveillance in West Africa, water quality monitoring, environmental microbe analysis, coronavirus SARS-CoV-2 diagnosis and even aboard the ISS [63][64][65][66][67][68][69][70][71]. The technique has also demonstrated to be reliable in resource-limited settings [69], a condition that is also verified for some cultural heritage monuments Worldwide.…”

“…Recently, Tamames and colleagues [71] developed and tested in volcanic rocks in La Palma, Canary Islands and marine waters, an in-situ system for Oxford Nanopore ® metagenomic analysis in less than one day. Understandably, with such progress, the application of the technique for on-site analysis can offer a wide range of possibilities in the cultural heritage biodeterioration area, such as the monitoring of microbial outbreaks and in the implementation of quick control measures [72,73].…”

“…Additionally, while the MinION™ sequencer offers portability and in-field analysis capabilities, sample preparation protocols may need optimization to ensure reproducibility and reliable results in non-laboratory settings. On the other hand, and to a lower degree, difficulties to conduct routinary procedures in situ, such as low DNA recovery from environmental samples, also needs to be noted [71]. Nonetheless, the system is one of the fastest developing NGS platforms today and their limitation are systematically being improved.…”