nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning

Krakau, Sabrina; Straub, Daniel; Gourlé, Hadrien; Gabernet, Gisela; Nahnsen, Sven

doi:10.1093/nargab/lqac007

Cited by 45 publications

(27 citation statements)

References 30 publications

(30 reference statements)

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“…Furthermore, reads were mapped individually in each sample. In future, new approaches based on assembling metagenomes by pooling reads from all samples might improve the analyses of the composition of the microbiome, while also enabling the recovery of the genome of community-shared strains that are not yet discovered (Uritskiy et al, 2018;Churcheward et al, 2022;Krakau et al, 2022). The DNA extraction protocol used was not specifically designed to target viral particles, which means that the abundance of bacteriophages might have been underestimated.…”

Section: Discussionmentioning

confidence: 99%

The association between the composition of the early-life intestinal microbiome and eczema in the first year of life

Leo¹,

Cetiner²,

Pittet³

et al. 2023

Front. Microbiomes

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IntroductionThe early-life intestinal microbiome plays a crucial role in the development and regulation of the immune system. Perturbations in its composition during this critical period have been linked to the development of allergic diseases.ObjectiveThis study aimed to investigate the association between the composition of the early-life intestinal microbiome and the presence of eczema in the first year of life using shotgun metagenomic sequencing and functional analyses (metabolic pathways).MethodsStool samples from 393 healthy term infants collected at 1 week of age were analyzed with shotgun metagenomic sequencing. Environmental and clinical data were prospectively collected using 3-monthly validated questionnaires. Participants were clinically assessed during study visits at 12 months of age. Eczema was diagnosed by the UK diagnostic tool and by a research nurse. Data analysis was stratified by delivery mode.ResultsEczema was diagnosed in 16.4% (60/366) of participants by nurse diagnosis. Infants born by cesarean section (CS) with nurse-diagnosed eczema had a higher relative abundance of Escherichia, Shigella, Enterobacter, and Citrobacter and a lower relative abundance of Veillonella than CS-born infants without eczema. In addition, CS-born infants without eczema had a higher abundance of genes involved in lactic fermentation. Vaginally born infants with eczema had a higher relative abundance of Bacteroides and a lower abundance of Streptococcus.ConclusionThere is an association between the bacterial composition of the intestinal microbiome at 1 week of age and the presence of eczema in the first 12 months of life.

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Section: Discussionmentioning

confidence: 99%

The association between the composition of the early-life intestinal microbiome and eczema in the first year of life

Leo¹,

Cetiner²,

Pittet³

et al. 2023

Front. Microbiomes

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“…Metagenomes were assembled using the Nextflow Core MAG pipeline (URL: nf-co.re/mag) [ 35 , 36 , 37 ]. Open reading frames (ORFs) were identified from each sample’s meta-assembly using Prodigal v. 2.63 [ 38 ] with the “normal” mode, which is the mode that identifies ORFs based on the start codons, end codons, and other properties that can be directly learned from the input sequences.…”

Section: Methodsmentioning

confidence: 99%

Gut Microbiome Changes Occurring with Norovirus Infection and Recovery in Infants Enrolled in a Longitudinal Birth Cohort in Leon, Nicaragua

Cannon

Seabolt

et al. 2022

Viruses

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Noroviruses are associated with one fifth of diarrheal illnesses globally and are not yet preventable with vaccines. Little is known about the effects of norovirus infection on infant gut microbiome health, which has a demonstrated role in protecting hosts from pathogens and a possible role in oral vaccine performance. In this study, we characterized infant gut microbiome changes occurring with norovirus-associated acute gastroenteritis (AGE) and the extent of recovery. Metagenomic sequencing was performed on the stools of five infants participating in a longitudinal birth cohort study conducted in León, Nicaragua. Taxonomic and functional diversities of gut microbiomes were profiled at time points before, during, and after norovirus infection. Initially, the gut microbiomes resembled those of breastfeeding infants, rich in probiotic species. When disturbed by AGE, Gammaproteobacteria dominated, particularly Pseudomonas species. Alpha diversity increased but the genes involved in carbohydrate metabolism and glycan biosynthesis decreased. After the symptoms subsided, the gut microbiomes rebounded with their taxonomic and functional communities resembling those of the pre-infection microbiomes. In this study, during disruptive norovirus-associated AGE, the gut microbiome was temporarily altered, returning to a pre-infection composition a median of 58 days later. Our study provides new insights for developing probiotic treatments and furthering our understanding of the role that episodes of AGE have in shaping the infant gut microbiome, their long-term outcomes, and implications for oral vaccine effectiveness.

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“…There are currently several assembly-based taxonomic software suites such as MG-RAST (Keegan et al, 2016), MMseqs2 (Mirdita et al, 2021), and a few that make use of a workflow language, including nf-core and Muffin written in Nextflow, and Atlas written in Snakemake (Di Tommaso et al, 2017;Kieser et al, 2020;Krakau et al, 2022;Mölder et al, 2021;Van Damme et al, 2021). The main advantage of MGP over MG-RAST is its ease of installation on local infrastructure, as it only requires running a setup script that downloads a supplied Singularity image from SylabsCloud, the latest version of Cromwell (Voss et al, 2022), Koalafam HMMER profiles (Takuya Aramaki et al, 2019), and the Swiss-Prot database (UniProt Consortium, 2018) which is converted to the DIAMOND aligner (Buchfink et al, 2015) format.…”

Section: Workflowmentioning

confidence: 99%

MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis

Shaban¹,

Quiroga²,

Turnbull³

et al. 2023

JOSS

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MetaGenePipe (MGP) is an efficient, flexible, portable, and scalable metagenomics pipeline that uses performant bioinformatics software suites and genomic databases to create an accurate taxonomic and functional characterization of the prokaryotic fraction of sequenced microbiomes. Written in the Workflow Definition Language (WDL), MGP produces output that can be explored and interpreted directly, or can be used for downstream analysis. MGP is a pipeline-development best practice tool that uses Singularity for containerization and includes a setup script that downloads the necessary databases for setup. The source code for MGP is freely available and distributed under the Apache 2.0 license. Gene prediction Prokaryotic predictionProdigal Starts file.starts.txt Nucleotide sequences .fa Protein translations .fa

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nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning

Cited by 45 publications

References 30 publications

The association between the composition of the early-life intestinal microbiome and eczema in the first year of life

The association between the composition of the early-life intestinal microbiome and eczema in the first year of life

Gut Microbiome Changes Occurring with Norovirus Infection and Recovery in Infants Enrolled in a Longitudinal Birth Cohort in Leon, Nicaragua

MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis

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