HackMDPublication figures and questions
General
- Describe datasets (samples, contig number + size, file size)
- Pipeline overview
- Describe run time + resources
- Maybe: give run time for different resource constellations
- Report/compare results of all tools (e.g. Venn diagrams)
Which antibiotics/secondary metabolites are in (meta)genomes?
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- Identify ARG-containing BGCs
- Possibly screen for duplications and HGT
- e.g. ARTS: Antibiotic Resistant Target Seeker (developed in 2016, not updated since 2019) 📖 https://doi.org/10.1093%2Fnar%2Fgkx360
- "Identification of Thiotetronic Acid Antibiotic Biosynthetic Pathways
by Target-directed Genome Mining" 📖 PDF - "Targeted antibiotic discovery through biosynthesis-associated resistance determinants: target directed genome mining" https://doi.org/10.1080/1040841X.2019.1590307
How to analyse new/underexplored taxa?
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Phylogeny of MAGs + annotation per MAG
Compare ARG class, amount, and/or diversity per MAG, e.g. in paper "Biosynthetic potential of the global ocean microbiome"
📖 https://doi.org/10.1038/s41586-022-04862-3
📖 https://doi.org/10.1016/j.scitotenv.2022.156178
- Which are unexplored lineages/peculiarities?
- Do sampling materials have an influence on ARG abundance etc.? Characterize samples in general (number of genes etc.)
- (Compare metatranscriptome expression?)
➡️ new targets for discovery of natural products/biosynthetic compounds
ARG and sample comparisons
Permutational Multivariate Analysis of Variance (PERMANOVA)
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What are differences of dataset parameters (in this figure water layers) influence sample ARG class composition?
📖 https://doi.org/10.1101/2021.01.20.427441 -
How do ARGs overlap within sample
📖 https://doi.org/10.1016/j.scitotenv.2022.156178 -
Compare relative abundance of ARGs from several datasets
📖 https://doi.org/10.1111/1758-2229.12453
Additional datasets
- List of publicly available metagenomic datasets: https://doi.org/10.1111/1758-2229.12453 (Table 1)
