gNOMO : a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms

© The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics..

The study of bacterial symbioses has grown exponentially in the recent past. However, existing bioinformatic workflows of microbiome data analysis do commonly not integrate multiple meta-omics levels and are mainly geared toward human microbiomes. Microbiota are better understood when analyzed in their biological context; that is together with their host or environment. Nevertheless, this is a limitation when studying non-model organisms mainly due to the lack of well-annotated sequence references. Here, we present gNOMO, a bioinformatic pipeline that is specifically designed to process and analyze non-model organism samples of up to three meta-omics levels: metagenomics, metatranscriptomics and metaproteomics in an integrative manner. The pipeline has been developed using the workflow management framework Snakemake in order to obtain an automated and reproducible pipeline. Using experimental datasets of the German cockroach Blattella germanica, a non-model organism with very complex gut microbiome, we show the capabilities of gNOMO with regard to meta-omics data integration, expression ratio comparison, taxonomic and functional analysis as well as intuitive output visualization. In conclusion, gNOMO is a bioinformatic pipeline that can easily be configured, for integrating and analyzing multiple meta-omics data types and for producing output visualizations, specifically designed for integrating paired-end sequencing data with mass spectrometry from non-model organisms.

Errataetall:

ErratumIn: NAR Genom Bioinform. 2020 Oct 09;2(4):lqaa083. - PMID 33577626

Medienart:

E-Artikel

Erscheinungsjahr:

2020

Erschienen:

2020

Enthalten in:

Zur Gesamtaufnahme - volume:2

Enthalten in:

NAR genomics and bioinformatics - 2(2020), 3 vom: 29. Sept., Seite lqaa058

Sprache:

Englisch

Beteiligte Personen:

Muñoz-Benavent, Maria [VerfasserIn]
Hartkopf, Felix [VerfasserIn]
Van Den Bossche, Tim [VerfasserIn]
Piro, Vitor C [VerfasserIn]
García-Ferris, Carlos [VerfasserIn]
Latorre, Amparo [VerfasserIn]
Renard, Bernhard Y [VerfasserIn]
Muth, Thilo [VerfasserIn]

Links:

Volltext

Themen:

Journal Article

Anmerkungen:

Date Revised 13.02.2021

published: Electronic-eCollection

ErratumIn: NAR Genom Bioinform. 2020 Oct 09;2(4):lqaa083. - PMID 33577626

Citation Status PubMed-not-MEDLINE

doi:

10.1093/nargab/lqaa058

funding:

Förderinstitution / Projekttitel:

PPN (Katalog-ID):

NLM321355172