SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline

Tamames, Javier; Puente-Sánchez, Fernando

doi:10.3389/fmicb.2018.03349

Cited by 278 publications

(223 citation statements)

References 47 publications

(45 reference statements)

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“…Functional and taxonomical profiling was obtained using the co-assembly procedure from SqueezeMeta automatic pipeline [27]. This method pools reads from all samples and a single shared assembly is defined.…”

Section: Dna Extractionmentioning

confidence: 99%

Taxonomical and Functional Assessment of the Endometrial Microbiota in A Context of Recurrent Reproductive Failure: A Case Report

et al. 2019

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Investigation of the microbial community in the female reproductive tract has revealed that the replacement of a community dominated by Lactobacillus with pathogenic bacteria may be associated with implantation failure or early spontaneous abortion in patients undergoing assisted reproductive technology (ART) treatment. Herein we describe taxonomically and functionally the endometrial microbiome of an infertile patient with repeated reproductive failures (involving an ectopic pregnancy and two clinical miscarriages). The microbiological follow-up is presented over 18-month in which the microbiota was evaluated in six endometrial fluid samples. The microbial profile of 16S rRNA gene sequencing showed a persistent infection with Gardnerella and other bacterial taxa such as Atopobium and Bifidobacterium. In addition, taxonomic and functional analysis by whole metagenome sequencing in the endometrial fluid sample collected before one clinical miscarriage suggested the presence of multiple Gardnerella vaginalis clades with a greater abundance of clade 4, usually associated with metronidazole resistance. These results revealed a persistent G. vaginalis endometrial colonization presenting genetic features consistent with antimicrobial resistance, biofilm formation, and other virulence factors, which could be related to the reproductive failure observed.

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Section: Dna Extractionmentioning

confidence: 99%

Taxonomical and Functional Assessment of the Endometrial Microbiota in A Context of Recurrent Reproductive Failure: A Case Report

et al. 2019

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“…Table 1 summarizes the number of bins generated, the assembly metrics, the total ORFs detected, the completeness-contamination of the bins, and the computational time used by DATMA. It also contrasts these results against the report produced by MetaWRAP (Uritskiy, DiRuggiero & Taylor, 2018) and SqueezeMeta (Tamames & Puente-Sánchez, 2019) frameworks. MetaWRAP completeness of the Brocadia genome is higher than the obtained by DATMA; but, DATMA obtains a better N50.…”

Section: Brocadia Caroliniensis Metagenomementioning

confidence: 58%

DATMA: Distributed AuTomatic Metagenomic Assembly and annotation framework

Benavides

Sánchez

Alzate

et al. 2020

PeerJ

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Background A prime objective in metagenomics is to classify DNA sequence fragments into taxonomic units. It usually requires several stages: read’s quality control, de novo assembly, contig annotation, gene prediction, etc. These stages need very efficient programs because of the number of reads from the projects. Furthermore, the complexity of metagenomes requires efficient and automatic tools that orchestrate the different stages. Method DATMA is a pipeline for fast metagenomic analysis that orchestrates the following: sequencing quality control, 16S rRNA-identification, reads binning, de novo assembly and evaluation, gene prediction, and taxonomic annotation. Its distributed computing model can use multiple computing resources to reduce the analysis time. Results We used a controlled experiment to show DATMA functionality. Two pre-annotated metagenomes to compare its accuracy and speed against other metagenomic frameworks. Then, with DATMA we recovered a draft genome of a novel Anaerolineaceae from a biosolid metagenome. Conclusions DATMA is a bioinformatics tool that automatically analyzes complex metagenomes. It is faster than similar tools and, in some cases, it can extract genomes that the other tools do not. DATMA is freely available at https://github.com/andvides/DATMA.

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“…ATCC 52814 (GCA_002083745.1) whole-genome sequence as a reference. The SqueezeMeta pipelines \cite{Tamames_2019} were employed for assembly, taxonomic, functional and bin analysis. The pipelines used co-assembly mode option where reads from all samples are pooled before the assembly using Megahit \cite{Li_2015} step performed.…”

Section: Methodsmentioning

confidence: 99%

Shotgun Metagenomic Analysis Reveals New Insights on Bacterial Community Profiles in Tempeh

Yulandi

Waturangi

Wahyudi

et al. 2020

Preprint

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11Objective: Amplicon sequencing targeted 16S ribosomal RNA (rRNA) has been widely used for the 12 analysis profile of the microbial community from fermented food samples. Previous results of 16S 13 rRNA analysis metagenome showed that Firmicutes was the dominant phylum in tempeh. However, 14 polymerase chain reaction (PCR) steps on amplicon sequencing analysis and intragenomic 15 heterogeneity within 16S rRNA are believed to contribute to bias in the estimation of microbial 16 community composition. An alternative approach known as shotgun metagenomic might be able to 17 avoid this limitation. In this study, we employed total metagenomic DNA fragments sequenced 18 directly for taxonomic dan functional profiling analysis. 19Result: Taxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the 20 dominant phyla from direct shotgun metagenomic analysis in all tempeh samples. In terms of 21 composition, the shotgun metagenomic study revealed that Proteobacteria was the most relatively 22 abundant phylum. Functional profiling showed that iron complex outer-membrane recepter protein 23 (KEGG ID: K02014) was the most transcribed genes based on metagenome from tempeh samples. 24 25 26 109 bacteria, Proteobacteria was the abundant phylum (Figure 1). Functional profiling used the latest 110 publicly version of KEGG database for KEGG ID annotation. Iron complex outer-membrane 111 recepter protein (KEGG ID: K02014) was the most transcripted expression in the metagenome from 112 tempeh samples (Figure 2). 113 Binning and Bin Check 114The total number of bins obtained from co-assembly metagenome EMP and WJB samples result 115 from DAS tool were 22. According to CheckM result, nine bins categorized as good-quality bins, 116 which completeness more than 75% with less than 10% contamination. Among good-quality bins, 117 six categorized as high-quality bins, which completeness more than 90% (Table 1). 118 119 Discussion 120 Study of the microbial community of EMP and WJB tempeh samples using 16S rRNA metagenome 121 sequencing analysis already conducted. Concordant with the result of shotgun metagenome 122 sequencing analysis in this study, Proteobacteria, Firmicutes, and Bacteroidetes were the abundant 123 phylum, although different in composition. Firmicutes relatively most abundant in amplicon 124 sequencing study while in a shotgun metagenomics study was Proteobacteria. The data expand the 125 understanding of bioprocess during soybean fermentation compare to previous microbial ecology 126 study using amplicon sequencing \cite{Kumar_2019, Sarkar_2002}.

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SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline

Cited by 278 publications

References 47 publications

Taxonomical and Functional Assessment of the Endometrial Microbiota in A Context of Recurrent Reproductive Failure: A Case Report

Taxonomical and Functional Assessment of the Endometrial Microbiota in A Context of Recurrent Reproductive Failure: A Case Report

DATMA: Distributed AuTomatic Metagenomic Assembly and annotation framework

Shotgun Metagenomic Analysis Reveals New Insights on Bacterial Community Profiles in Tempeh

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