## Publication 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? :arrow_right: Targeted ARG/BGC identification - 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](https://pubs.acs.org/doi/pdf/10.1021/acschembio.5b00658) - "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? :arrow_right: Taxonomic distribution of ARGs :arrow_right: Identify gene-rich lineages, characterize them #### 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" ![genes per MAG/genome 1](https://i.imgur.com/Zr2S3N8.png) 📖 https://doi.org/10.1038/s41586-022-04862-3 ![genes per MAG/genome 2](https://i.imgur.com/jhwraAy.png) 📖 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) - What are differences of dataset parameters (in this figure water layers) influence sample ARG class composition? ![sample comparison](https://i.imgur.com/nVLlj0s.png) 📖 https://doi.org/10.1101/2021.01.20.427441 - How do ARGs overlap within sample ![ARG overlap](https://i.imgur.com/ZH8dTsP.png) 📖 https://doi.org/10.1016/j.scitotenv.2022.156178 - Compare relative abundance of ARGs from several datasets ![ARG abundance and dataset heatmap](https://i.imgur.com/moUSMGm.png) 📖 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)