ArticleBriefings in bioinformatics2021
Functional meta-omics provide critical insights into long- and short-read assemblies.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 13 citations in OpenAlex.
- Metagenomic assemblies tend to break around antibiotic resistance genes.BMC genomics · 2024Article
- Deciphering Microbiome, Transcriptome, and Metabolic Interactions in the Presence of ProbioticAntibiotics (Basel, Switzerland) · 2024Article
- Dancing the Nanopore limbo - Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction.BMC genomics · 2023Article
- The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020).Journal of biomolecular techniques : JBT · 2023Article
- Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes.Briefings in bioinformatics · 2023Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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