Dataset Information

Synergistic effect of short- and long-read sequencing on functional meta-omics

ABSTRACT: Evaluation of short-read-only, long-read-only, and hybrid assembly approaches on metagenomic samples demonstrating how they affect gene and protein prediction which is relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic, and metaproteomic data to evaluate the metagenomic-based protein predictions.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Human Gut Metagenome

SUBMITTER: Benoit Kunath

LAB HEAD: Paul Wilmes

PROVIDER: PXD025505 | Pride | 2022-02-17

REPOSITORIES: Pride

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Publications

Functional meta-omics provide critical insights into long- and short-read assemblies.

Galata Valentina V Busi Susheel Bhanu SB Kunath Benoît Josef BJ de Nies Laura L Calusinska Magdalena M Halder Rashi R May Patrick P Wilmes Paul P Laczny Cédric Christian CC

Briefings in bioinformatics 20211101 6

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 complementar ...[more]

PMID: 34453168

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Project description:Characterization of microbial communities at the genomic, transcriptomic, proteomic and metabolomic levels, with a special interest on lipid accumulating bacterial populations, which are naturally enriched in biological wastewater treatment systems and may be harnessed for the conversion of mixed lipid substrates (wastewater) into biodiesel. The project aims to elucidate the genetic blueprints and the functional relevance of specific populations within the community. It focuses on within-population genetic and functional heterogeneity, trying to understand how fine-scale variations contribute to differing lipid accumulating phenotypes. Insights from this project will contribute to the understanding the functioning of microbial ecosystems, and improve optimization and modeling strategies for current and future biological wastewater treatment processes. This project contains datasets derived from the same biological wastewater treatment plant. The data includes metagenomes, metatranscriptomes, metaproteomes and organisms isolated in pure cultures. Characterization of microbial communities at the genomic, transcriptomic, proteomic and metabolomic levels, with a special interest on lipid accumulating bacterial populations, which are naturally enriched in biological wastewater treatment systems and may be harnessed for the conversion of mixed lipid substrates (wastewater) into biodiesel. The project aims to elucidate the genetic blueprints and the functional relevance of specific populations within the community. It focuses on within-population genetic and functional heterogeneity, trying to understand how fine-scale variations contribute to differing lipid accumulating phenotypes. Insights from this project will contribute to the understanding the functioning of microbial ecosystems, and improve optimization and modeling strategies for current and future biological wastewater treatment processes. This project contains datasets derived from the same biological wastewater treatment plant. The data includes metagenomes, metatranscriptomes, metaproteomes and organisms isolated in pure cultures.

Dataset Information

Synergistic effect of short- and long-read sequencing on functional meta-omics

Publications

Functional meta-omics provide critical insights into long- and short-read assemblies.

Similar Datasets

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