Lactobacillus genus taxonomy

This repository contains code to analyze the genus-level (and family-level) taxonomy of the Lactobacillus Genus Complex (families Lactobacillaceae and Leuconostocaceae).

The results of these analyses have been published in IJSEM:

Zheng, J., Wittouck, S., Salvetti, E., Franz, C. M. A. P., Harris, H. M. B., Mattarelli, P., O’Toole, P. W., Pot, B., Vandamme, P., Walter, J., Watanabe, K., Wuyts, S., Felis, G. E., Gänzle, M. G., & Lebeer, S. (2020). A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. International Journal of Systematic and Evolutionary Microbiology. https://doi.org/https://doi.org/10.1099/ijsem.0.004107

Data

From the legen pipeline, version 3.4:

• genome_pairs.csv.zip: data_v3/similarities/genome_pairs.csv.zip
• genomes_clusters.csv: data_v3/genome_clusters/genomes_clusters.csv
• clusters_all_named.csv: data_v3/taxonomy/clusters_all_named.csv
• outgroup_genomes.tsv: data_v3/outgroups/outgroup_genomes.tsv
• pangenome_legen_v3_3: data_v3/representatives_v3_3/pangenome/OrthoFinder/Orthogroups/
• lacto_dna.treefile: data_v3/representatives_v3_3/tree_dna/lacto_dna.treefile
• lacto_protein.treefile: data_v3/representatives_v3_3/tree_protein/lacto_protein.treefile
• lacto_gc.treefile: data_v3/representatives_v3_3/tree_gc/lacto_gc.treefile

Other data:

• lactobacillaceae_genera_2019.csv: constructed manually using the IJSEM manuscript; the column order_phylogeny is based on figure 5
• table_S1_corrected:
  • downloaded from https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004107#supplementary_data
  • deleted row 158 (exact duplicate of row 149; Lactobacillus mulieris)
  • cell C53: changed to "Lactobacillus algidus" (added genus name)
  • cell O53: changed to "Dellaglioa algida" (added genus name)
  • cell C245: changed to "Lactobacillus aquaticus" (removed the single quote)
  • cell O324: changed to "Pediococcus acidilactici" (added genus name)
  • cells C300 - C304: fixed double spaces
• table_S3:
  • downloaded from https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004107#supplementary_data
• table_S4:
  • downloaded from https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004107#supplementary_data

Scripts

All scripts can be found in the src folder:

• 00_adapt_species names.R: make some slight changes to the species names (compared to the legen pipeline)
• 01_visualize_repr_trees.R: visualize various phylogenetic trees of representative genomes of LGC species
• 02_explore_signature_genes.R: explore signature genes (core and exclusive genes for a clade) in the LGC
• 03_explore_classification.R: explore how new genomes can be classified on the genus level in the new taxonomy