The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements

Browne, Patrick; Kot, Witold; Jørgensen, Tue Sparholt; Hansen, Lars Hestbjerg

doi:10.1007/978-1-4939-9877-7_18

Cited by 6 publications

(5 citation statements)

References 34 publications

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“…For the plasmid dataset, inlet wastewater from a wastewater treatment plant on Zealand, Denmark was used to generate a plasmid sample similar to ref. 64 . Sequencing was performed on a NextSeq 500 on Nextera sequencing libraries (Illumina).…”

Section: Methodsmentioning

confidence: 99%

Critical Assessment of Metagenome Interpretation: the second round of challenges

et al. 2022

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Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.

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Section: Methodsmentioning

confidence: 99%

Critical Assessment of Metagenome Interpretation: the second round of challenges

et al. 2022

Self Cite

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“…For the plasmid dataset, inlet wastewater from a wastewater treatment plant on Zealand, Denmark was used to generate a plasmid sample similar to the procedure in 77 .…”

Section: Genome Sequencing and Assemblymentioning

confidence: 99%

“…76 Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany. 77 Technische Universität Braunschweig, Braunschweig, Germany.…”

mentioning

confidence: 99%

Critical Assessment of Metagenome Interpretation - the second round of challenges

Meyer

Fritz

Deng

et al. 2021

Preprint

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Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the community to assess their methods on realistic and complex metagenomic datasets with long and short reads, created from ∼1,700 novel and known microbial genomes, as well as ∼600 novel plasmids and viruses. Altogether 5,002 results by 76 program versions were analyzed, representing a 22x increase in results.Substantial improvements were seen in metagenome assembly, some due to using long-read data. The presence of related strains still was challenging for assembly and genome binning, as was assembly quality for the latter. Taxon profilers demonstrated a marked maturation, with taxon profilers and binners excelling at higher bacterial taxonomic ranks, but underperforming for viruses and archaea. Assessment of clinical pathogen detection techniques revealed a need to improve reproducibility. Analysis of program runtimes and memory usage identified highly efficient programs, including some top performers with other metrics. The CAMI II results identify current challenges, but also guide researchers in selecting methods for specific analyses.

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“…Interestingly, Herning sand filter communities showed a higher mobilizing potential than those of Kerteminde and Bregnerød, suggesting that the presence of compatible conjugative elements may be variable across sand filters. Together, these results highlight the relevance of designing parallel meta-mobilome studies to investigate the indigenous pool of MGEs ( 42 , 43 ). Such studies would enable a deeper understanding of the factors affecting the plasmid transfer potential of exogenous plasmids within complex microbial communities.…”

Section: Resultsmentioning

confidence: 79%

Broad Dissemination of Plasmids across Groundwater-Fed Rapid Sand Filter Microbiomes

Pinilla‐Redondo

Olesen

Russel

et al. 2021

mBio

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The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements

Cited by 6 publications

References 34 publications

Critical Assessment of Metagenome Interpretation: the second round of challenges

Critical Assessment of Metagenome Interpretation: the second round of challenges

Critical Assessment of Metagenome Interpretation - the second round of challenges

Broad Dissemination of Plasmids across Groundwater-Fed Rapid Sand Filter Microbiomes

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