MetaStorm: A Public Resource for Customizable Metagenomics Annotation

Arango-Argoty, Gustavo; Singh, Gargi; Heath, Lenwood S.; Pruden, Amy; Xiao, Weidong; Zhang, Liqing

doi:10.1371/journal.pone.0162442

Cited by 56 publications

(52 citation statements)

References 49 publications

(70 reference statements)

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“…( 2015 ) (Arango-Argoty et al. 2016 ). For putative pathogens, relative abundances of individual species were derived from MetaPhlan2 and cross-referenced to bacterial pathogens housed in the PATRIC database (Truong et al.…”

Section: Methodsmentioning

confidence: 99%

MetaCompare: a computational pipeline for prioritizing environmental resistome risk

Pruden

Chen

et al. 2018

FEMS Microbiology Ecology

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The spread of antibiotic resistance is a growing public health concern. While numerous studies have highlighted the importance of environmental sources and pathways of the spread of antibiotic resistance, a systematic means of comparing and prioritizing risks represented by various environmental compartments is lacking. Here, we introduce MetaCompare, a publicly available tool for ranking ‘resistome risk’, which we define as the potential for antibiotic resistance genes (ARGs) to be associated with mobile genetic elements (MGEs) and mobilize to pathogens based on metagenomic data. A computational pipeline was developed in which each ARG is evaluated based on relative abundance, mobility, and presence within a pathogen. This is determined through the assembly of shotgun sequencing data and analysis of contigs containing ARGs to determine if they contain sequence similarity to MGEs or human pathogens. Based on the assembled metagenomes, samples are projected into a 3-dimensionalhazard space and assigned resistome risk scores. To validate, we tested previously published metagenomic data derived from distinct aquatic environments. Based on unsupervised machine learning, the test samples clustered in the hazard space in a manner consistent with their origin. The derived scores produced a well-resolved ascending resistome risk ranking of: wastewater treatment plant effluent, dairy lagoon, and hospital sewage.

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Section: Methodsmentioning

confidence: 99%

MetaCompare: a computational pipeline for prioritizing environmental resistome risk

Pruden

Chen

et al. 2018

FEMS Microbiology Ecology

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“…The recently developed Carnelian [168] tool is recommended to perform comparative functional metagenomics. Further, more flexible tools enabling customizable annotation, such as MetaStorm [169], a web server that supports read or assembly annotation based on a reference dataset uploaded by the users, have been developed. This also provides enhanced interactive visualization and outperforms previous tools.…”

Section: Wgs Metagenomicsmentioning

confidence: 99%

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

2020

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Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.

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“…Various bioinformatics approaches are under development to identify and classify ARGs that are obtained from shot-gun metagenomics sequencing, but are limited both by the length and quality of the read as well as the quality of available databases for identifying the sequences. Currently, several databases and pipelines are available to identify ARGs, MGEs, and other genes of interest [46][47][48], but there is need for improved curation and standardization for comparability purposes. New sequencing platforms, like PacBio, that provide long read lengths are now available and provide richer information for gene identification and also advance confidence in assembly.…”

Section: Monitoring and Surveillance Of Antibiotic Resistancementioning

confidence: 99%

Reusing Treated Wastewater: Consideration of the Safety Aspects Associated with Antibiotic-Resistant Bacteria and Antibiotic Resistance Genes

Hong

Julian

Pype

et al. 2018

Water

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As more countries engage in water reuse, either intended or de facto, there is an urgent need to more comprehensively evaluate resulting environmental and public health concerns. While antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are increasingly coming under the spotlight, as emerging contaminants, existing water reuse regulations and guidelines do not adequately address these concerns. This perspectives paper seeks to frame the various challenges that need to be resolved to identify meaningful and realistic target types and levels of antibiotic resistance benchmarks for water reuse. First, there is the need for standardized and agreed-upon methodologies to identify and quantify ARB and ARGs. Second, even if methodologies are available, identifying which ARB and ARGs to monitor that would best relate to the occurrence of disease burden remains unknown. Third, a framework tailored to assessing the risks associated with ARB and ARGs during reuse is urgently needed. Fourth, similar to protecting drinking water sources, strategies to prevent dissemination of ARB and ARGs via wastewater treatment and reuse are required to ensure that appropriate barriers are emplaced. Finally, current wastewater treatment technologies could benefit from modification or retrofit to more effectively remove ARB and ARGs while also producing a high quality product for water and resource recovery. This perspectives paper highlights the need to consider ARB and ARGs when evaluating the overall safety aspects of water reuse and ways by which this may be accomplished.

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MetaStorm: A Public Resource for Customizable Metagenomics Annotation

Cited by 56 publications

References 49 publications

MetaCompare: a computational pipeline for prioritizing environmental resistome risk

MetaCompare: a computational pipeline for prioritizing environmental resistome risk

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

Reusing Treated Wastewater: Consideration of the Safety Aspects Associated with Antibiotic-Resistant Bacteria and Antibiotic Resistance Genes

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