Alexandre Jousset

If you’re interested in rapid in-situ metagenomics with Oxford @nanopore MinION, here’s a great example of how a lab-in-a-suitcase approach can achieve same-day on-site results, allowing “real-time functional and taxonomic monitoring of microbial communities in remote areas”. The article, by Tamames et al. (2024), features two case studies: ⭐Investigating the microbial communities associated with volcanic rocks on La Palma island, Canary Islands, Spain. Here the authors investigated bacterial and eukaryotic communities on lava rocks of different ages, producing results within a 24-hour window. To validate the results, the data produced with ONT MinION were later compared with those produced with Illumina NextSeq2000. The taxa and functional genes detected with both sequencing technologies were very similar, confirming the results were accurate. ⭐ Investigating the sulphur metabolism genes in planktonic microbial communities in Ria de Vigo, an estuary in Galicia, Spain. In this study the aim was to test a results-driven sampling approach over two days. On the first day surface waters were sampled and analysed from three sites, with the results indicating the most interesting site for sulphur metabolism genes to be sampled and analysed in greater detail during the second day. The authors suggest several advantages of their in-situ approach, such as: 🧬 Rapid monitoring of microbial communities: where rapid results can guide rapid appropriate responses, for example pathogen and antimicrobial resistance gene detection, rapidly evolving microbial blooms, fermentations, and bioreactors. 🧬 Rapid surveys of remote sites: where rapid results can allow researchers to determine whether a site is of interest or not, and whether to sample in more depth or sample elsewhere. 🧬 Rapid discussion of results: the authors' software pipeline allows immediate publishing of the results on a web interface (provided there is an internet connection) allowing collaborators elsewhere in the world to access and interrogate the results as if they were present. Very cool stuff! You can read the article here: Tamames et al. (2024). In situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day. Molecular Ecology Resources, 24(2), e13909. onlinelibrary.wiley.com/doi/… You can also find a complete experimental protocol to accompany the article here: github.com/jtamames/In-situ-…