Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines

Valencia, E. Michael; Maki, Katherine A.; Dootz, Jennifer N.; Barb, Jennifer J.

doi:10.1038/s41597-023-02877-7

Cited by 2 publications

References 98 publications

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Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities

Van Uffelen,

Posadas,

Roosens

et al. 2024

Sci Data

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Taxonomic classification is crucial in identifying organisms within diverse microbial communities when using metagenomics shotgun sequencing. While second-generation Illumina sequencing still dominates, third-generation nanopore sequencing promises improved classification through longer reads. However, extensive benchmarking studies on nanopore data are lacking. We systematically evaluated performance of bacterial taxonomic classification for metagenomics nanopore sequencing data for several commonly used classifiers, using standardized reference sequence databases, on the largest collection of publicly available data for defined mock communities thus far (nine samples), representing different research domains and application scopes. Our results categorize classifiers into three categories: low precision/high recall; medium precision/medium recall, and high precision/medium recall. Most fall into the first group, although precision can be improved without excessively penalizing recall with suitable abundance filtering. No definitive ‘best’ classifier emerges, and classifier selection depends on application scope and practical requirements. Although few classifiers designed for long reads exist, they generally exhibit better performance. Our comprehensive benchmarking provides concrete recommendations, supported by publicly available code for reassessment and fine-tuning by other scientists.

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Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities

Van Uffelen,

Posadas,

Roosens

et al. 2024

Sci Data

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Jellyfish blooms - an overlooked hotspot and potential vector for the transmission of antimicrobial resistance in marine environments

Elena,

Orel,

Fang

et al. 2024

Preprint

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Jellyfish, and gelatinous zooplankton (GZ) in general, represent an important component of marine food webs. Certain GZ species are capable of generating massive blooms of severe environmental impact. These blooms are often followed by a sudden collapse of the entire population, introducing considerable amounts of organic matter (GZ-OM) in the ocean’s interior. GZ-OM represents an abundant substrate to promote bacterial growth and copious colonizable surface for microbial interactions. Hence we hypothesized that this GZ-OM serves as a yet overlooked hotspot for transmitting antimicrobial resistance genes (ARGs) in marine environments. For this we experimentally evolved and analyzed marine microbial communities in microcosms in presence and absence of OM from scyphozoanAurelia auritas.l. and ctenophoreMnemiopsis leidyi. Communities evolved under GZ-OM exposure displayed an up to 4-fold increase in relative ARG and an up to 10-fold increase in abundance of horizontally transferable mobile genetic elements (MGEs) per 16S rRNA gene copy compared to the controls. This trait was consistent across ARG and MGE classes and independent of the GZ species, suggesting that the underlying mechanism is indeed based on the general influx of nutrients and colonizable surfaces. Potential ARG carriers included known key GZ-OM degraders, but also genera containing potential pathogens hinting towards an increased risk of ARG transfer to pathogenic strains. Here,Vibriowere pinpointed as potential key species directly associated with several significantly elevated ARGs and MGEs. Subsequent whole-genome sequencing of aVibrioisolate from the microcosm experiment revealed the genetic potential for the mobilization and transfer of ARGs in GZ-OM degrading microbial consortia. With this study, we established the first link between two emerging issues of marine coastal zones, jellyfish blooms and AMR spread, both likely increasing in projected future ocean scenarios.

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Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines

Cited by 2 publications

References 98 publications

Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities

Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities

Jellyfish blooms - an overlooked hotspot and potential vector for the transmission of antimicrobial resistance in marine environments

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