In 2020, two taxonomic changes to the family Lactobacillaceae were published in IJSEM: (1) the merger of the family Leuconostocaceae into Lactobacillaceae and (2) the split of the genus Lactobacillus into 25 separate genera (one of which retained the name Lactobacillus). This taxonomic change increased the taxonomic resolution of 16S rRNA amplicon sequencing studies, as sequences can now be classified to smaller, more meaningful genera. Here we provide code that can be used to reclassify the Lactobacillaceae sequences present in an amplicon dataset (where reference sequences of ASVs/OTUs are still present) to the new taxonomy.
A demonstration of a reclassification can be found in src/demonstration.R.
The necessary datasets and the reference database for classification can be downloaded by running src/download_datasets.sh.
- R version 4.1.1
- R packages:
- tidyverse version 1.3.1
- tidyamplicons version 0.2.2
- dada2 version 1.20.0
ferme_pekes_preprocessed
- samples from carrot juice fermentations that volunteers did at home
- amplicon: V4 region of the 16S rRNA gene
- from this study
isala_pilot_amplicon_preprocessed
- vaginal samples from volunteers (not taken in a clinical context)
- amplicon: V4 region of the 16S rRNA gene
- from this study