PlasClass improves plasmid sequence classification

Pellow, David; Mizrahi, Itzik; Shamir, Ron

doi:10.1101/783571

Cited by 20 publications

(44 citation statements)

References 8 publications

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“…We compared PCS versus PlasClass (Pellow, Mizrahi, and Shamir 2020) , a recent method that also fits a logistic regression but uses k-mers of length 3-7 as features, in their ability to classify the 10kb sequences. We did not compare with other k-mer methods (Krawczyk, Lipinski, and Dziembowski 2018;Zhou and Xu 2010) because the PlasClass study reported better performance than them.…”

Section: Pcs: a State-of-the-art Plasmid Classifier System Based On Gmentioning

confidence: 99%

The genetic and ecological landscape of plasmids in the human gut

Fogarty

Eren

2020

Preprint

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Plasmids play a critical role in rapid bacterial adaptation by encoding accessory functions that may increase the host's fitness. However, the diversity and ecology of plasmids is poorly understood due to computational and experimental challenges in plasmid identification. Here, we report the Plasmid Classification System (PCS), a machine learning classifier that recognizes plasmid sequences based on gene functions. To train PCS, we performed a large-scale discovery and comparison of gene functions in a reference set of >16,000 plasmids and >14,000 chromosomes. PCS accurately recognizes a diverse range of plasmid subtypes, and it outperforms the previous state-of-the-art approach based on k-mer decomposition of sequences. Armed with this model, we conducted, to our knowledge, the largest search for naturally occurring human gut plasmids in 406 publicly available metagenomes representing 5 countries. This search yielded 6,257 high-confidence predicted plasmids, of which 576 had evidence of a circular conformation based on pair-end mapping. These predicted plasmids were found to be highly prevalent across the metagenomes compared to the reference set of known plasmids, suggesting there is extensive and uncharacterized plasmid diversity in the human gut microbiome.

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Section: Pcs: a State-of-the-art Plasmid Classifier System Based On Gmentioning

confidence: 99%

The genetic and ecological landscape of plasmids in the human gut

Fogarty

Eren

2020

Preprint

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“…Many bioinformatic tools have been recently developed to overcome this challenge in short-read sequencing. Examples of them are PlasmidFinder, cBar, PLACNET, (meta)plasmidSPAdes, recycler, plasflow, MOB-suite, mlplasmids, plaScope, gplas, plasClass, plasGUN,SCAPP, metaviralSPAdes ( Zhou and Xu, 2010 ; Carattoli et al., 2014 ; Rozov et al., 2017 ; Vielva et al., 2017 ; Arredondo-Alonso et al., 2018 ; Arredondo-Alonso et al., 2020 ; Krawczyk et al., 2018 ; Robertson and Nash, 2018 ; Royer et al., 2018 ; Antipov et al., 2019 , 2020 ; Fang et al., 2020 ; Pellow et al., 2020a , Pellow et al., 2020b ; Pellow et al., 2020 , 2020 ). These tools identify plasmids and viruses in metagenomic samples or bacterial isolates in a variety of ways, ranging from the simpler approach of blasting against a plasmid database (PlasmidFinder, MOB-suite) to the use of more complex deep neural networks (cBar, PlasFlow).…”

Section: Methods For Mobile Genetic Elements Analysis In Environmentamentioning

confidence: 99%

The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

2020

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Wastewater treatment plants (WWTPs) are crucial for producing clean effluents from polluting sources such as hospitals, industries, and municipalities. In recent decades, many new organic compounds have ended up in surface waters in concentrations that, while very low, cause (chronic) toxicity to countless organisms. These organic micropollutants (OMPs) are usually quite recalcitrant and not sufficiently removed during wastewater treatment. Microbial degradation plays a pivotal role in OMP conversion. Microorganisms can adapt their metabolism to the use of novel molecules via mutations and rearrangements of existing genes in new clusters. Many catabolic genes have been found adjacent to mobile genetic elements (MGEs), which provide a stable scaffold to host new catabolic pathways and spread these genes in the microbial community. These mobile systems could be engineered to enhance OMP degradation in WWTPs, and this review aims to summarize and better understand the role that MGEs might play in the degradation and wastewater treatment process. Available data about the presence of catabolic MGEs in WWTPs are reviewed, and current methods used to identify and measure MGEs in environmental samples are critically evaluated. Finally, examples of how these MGEs could be used to improve micropollutant degradation in WWTPs are outlined. In the near future, advances in the use of MGEs will hopefully enable us to apply selective augmentation strategies to improve OMP conversion in WWTPs.

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“…By default, we use PlasClass (Pellow et al, 2019) to annotate each node in the assembly graph with a plasmid score. PlasFlow (Krawczyk et al, 2018) scores are also supported.…”

Section: Plasmid Score Annotationmentioning

confidence: 99%

“…The peeling may reduce coverage of each involved node, or remove it altogether. In SCAPP the assembly graph is annotated with plasmid-specific genes and a plasmid score based on a plasmid sequence classifier (Pellow et al, 2019). In the annotated assembly graph we prioritize circular paths that include plasmid genes and highly probable plasmid sequences.…”

Section: Introductionmentioning

confidence: 99%

SCAPP: An algorithm for improved plasmid assembly in metagenomes

Pellow

Zorea

Probst

et al. 2020

Preprint

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Motivation: Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids, which are less studied or understood. In order to assist in the study of these plasmids we developed SCAPP (Sequence Contents Aware Plasmid Peeler) -an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. Results: SCAPP builds on some key ideas from the Recycler plasmid assembly algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome that we generated. We also created a parallel plasmidome-metagenome cow rumen sample and used it to create a novel assessment procedure. In most cases SCAPP performed better than or similar to Recycler and meta-plasmidSPAdes across this wide range of datasets. Availability: https://github.com/Shamir-Lab/SCAPP

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PlasClass improves plasmid sequence classification

Cited by 20 publications

References 8 publications

The genetic and ecological landscape of plasmids in the human gut

The genetic and ecological landscape of plasmids in the human gut

The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

SCAPP: An algorithm for improved plasmid assembly in metagenomes

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