Article (Scientific journals)
Functional meta-omics provide critical insights into long- and short-read assemblies
Galata, Valentina; Busi, Susheel Bhanu; Kunath, Benoît et al.
2021In Briefings in Bioinformatics
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Valentina Galata and Susheel Bhanu Busi Equal contribution. © The Author(s) 2021. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.


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Keywords :
third-generation sequencing; long reads; Oxford Nanopore Technologies; hybrid assembly; functional omics; meta-omics
Abstract :
[en] Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artifacts from genes and proteins present in situ. Here, we evaluate short-read-only, long-read-only and hybrid assembly approaches on four different metagenomic samples of varying complexity. We demonstrate how different assembly approaches affect gene and protein inference, which is particularly relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic and metaproteomic data to assess the metagenomic data-based protein predictions. Our findings pave the way for critical assessments of metagenomic reconstructions. We propose a reference-independent solution, which exploits the synergistic effects of multi-omic data integration for the in situ study of microbiomes using long-read sequencing data.
Research center :
Luxembourg Centre for Systems Biomedicine (LCSB)
Disciplines :
Microbiology
Author, co-author :
Galata, Valentina ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
Busi, Susheel Bhanu ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
Kunath, Benoît ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
de Nies, Laura ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
Calusinska, Magdalena ;  University of Luxembourg
Halder, Rashi ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Scientific Central Services
May, Patrick  ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core
Wilmes, Paul ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
Laczny, Cedric Christian  ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
External co-authors :
no
Language :
English
Title :
Functional meta-omics provide critical insights into long- and short-read assemblies
Publication date :
27 August 2021
Journal title :
Briefings in Bioinformatics
ISSN :
1477-4054
Publisher :
Oxford University Press, United Kingdom
Peer reviewed :
Peer Reviewed verified by ORBi
Focus Area :
Systems Biomedicine
FnR Project :
FNR11823097 - Microbiomes In One Health, 2017 (01/09/2018-28/02/2025) - Paul Wilmes
Funders :
FNR - Fonds National de la Recherche [LU]
SNSF - Swiss National Science Foundation [CH]
CER - Conseil Européen de la Recherche [BE]
Probiotics in External Applications (PBGL)
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