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In-situ metagenomics: A platform for on-field rapid sequencing and analysis of metagenomes in less than one day
  • +2
  • Javier Tamames,
  • Diego Jiménez-Lalana,
  • Alvaro Redondo,
  • Sandra Martínez-García,
  • Asunción de los Ríos
Javier Tamames
Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC)

Corresponding Author:[email protected]

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Diego Jiménez-Lalana
Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC)
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Alvaro Redondo
Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC)
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Sandra Martínez-García
Universidade de Vigo
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Asunción de los Ríos
Museo Nacional de Ciencias Naturales
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Abstract

We present a complete portable pipeline for sequencing and analysis of environmental metagenomes in less than a 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. Finally, 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 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 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 profiling of microbial communities in remote areas
22 Aug 2023Submitted to Molecular Ecology Resources
24 Aug 2023Submission Checks Completed
24 Aug 2023Assigned to Editor
24 Aug 2023Review(s) Completed, Editorial Evaluation Pending
02 Sep 2023Reviewer(s) Assigned
06 Oct 2023Editorial Decision: Revise Minor
03 Nov 20231st Revision Received
15 Nov 2023Submission Checks Completed
15 Nov 2023Assigned to Editor
15 Nov 2023Review(s) Completed, Editorial Evaluation Pending
21 Nov 2023Editorial Decision: Accept