Defining the cultured and uncultured bacterial fractions in Cannabis seeds

Authors: Carolina Lobato, Ahmed Abdelfattah, Gabriele Berg & Tomislav Cernava

Institute of Environmental Biotechnology (UBT) — TU Graz

Project structure

project/
├── data/
│   ├── lima/
│   │   ├── lima-bc.fasta
│   │   └── biosamples.csv
│   ├── r/
│   │   └── metadata.csv
│   ├── galaxy/
│   │   ├── bh_amp.fasta
│   │   └── bh_pb.fasta
│   ├── megax/
│   │   ├── bh_pb.fasta
│   │   └── bh_pb.meg
│   ├── itol/
│   │   ├── bh_pb-asgn.csv
│   │   ├── bh_pb-genus.csv
│   │   └── bh_pb-class.csv
│   ├── julia/
│   │   ├── asv-table-fw.csv
│   │   └── metadata-fw.csv
│   └── cytoscape/
│       ├── nodes-rel-rec.csv
│       └── nodes-taxa.csv
│
├── scripts/
│   ├── r/
│   │   ├── 1-dada2.Rmd
│   │   ├── 2-setup.Rmd
│   │   ├── Fig_1.Rmd
│   │   ├── Fig_2.Rmd
│   │   ├── Fig_3.Rmd
│   │   └── Fig_4.Rmd
│   └── utils/
│       ├── demux-lima.txt
│       ├── 0-install.R 
│       └── flashweave.jl
│
├── outputs/       
│   ├── r/
│   │   ├── 1-dada2
│   │   ├── 2-setup
│   │   ├── Fig_1
│   │   ├── Fig_2
│   │   ├── Fig_3
│   │   ├── Fig_4
│   │   └── SI
│   ├── galaxy/
│   │   └── mb-cov100.txt
│   ├── megax/
│   │   └── bh_pb_phytree99.nwk
│   ├── julia/
│   │   ├── nw_hetero_n20_a05_mk3.gml
│   │   └── nodes-hetero-n20-a05-mk3.csv
│   └── cytoscape/
│       └── fw_hetero_n20_a05_mk3.cys
│
├── README.md
└── LICENSE

Details

• data/

  • lima/ This subdirectory contains:
    • barcode file (lima-bc.fasta).
    • sample IDs (biosamples.csv).
  • r/ This subdirectory contains:
    • sample information (metadata.csv).
  • galaxy/ This subdirectory contains:
    • sequences from Lobato et al., 2024 used as query in Galaxy (bh_amp.fasta).
    • sequences from cultured taxa used as a database in Galaxy (bh_pb.fasta)
  • megax/ This subdirectory contains:
    • aligned sequences from cultured taxa obtained from bh_pb.fasta and used for maximum likelihood tree construction (bh_pb.meg)
  • itol/ This subdirectory contains:
    • annotations on genus level for each cultured ASV (bh_pb-genus.txt)
    • annotations on class level for each cultured ASV (bh_pb-class.txt)
    • annotations on the number of assignments at >99% similarity between community and cultured sequences (bh_pb-asgn.txt)
  • julia/ This subdirectory contains:
    • feature table (asv-table-fw.csv).
    • sample information (metadata-fw.csv).
  • cytoscape/ This subdirectory contains:
    • ASV mean relative abundance and identification of cultured ASVs (nodes-rel-rec.csv).
    • ASV taxonomic information (nodes-taxa.csv).

• scripts/

  • r/ This subdirectory contains the scripts used in R to create the phyloseq objects, preprocess the data, and prepare the figures for the manuscript.
  • utils/ This subdirectory contains utility scripts such as:
    • 0-install.R, for installing the necessary packages in R.
    • demux-lima.txt, which contains the script for demultiplexing CCS/HiFi reads using Lima.
    • flashweave.jl contains the script for building the network using Flashweave.

• outputs/ contains saved outputs.

Further content

The 16S Pacbio V1-V9 rRNA gene amplicon raw FASTQ files for Cannabis cultured seed endophytic bacterial taxa were deposited in ENA under the accession number PRJEB83654.

References

Lobato, C. et al. Defining the cultured and uncultured bacterial fractions in Cannabis seeds. Environmental Microbiome 20, 68 (2025). https://doi.org/10.1186/s40793-025-00731-4