chem16S

Chemical metrics of 16S rRNA-based community reference proteomes

This R package combines taxonomic classifications of high-throughput 16S rRNA gene sequences with reference proteomes of archaea and bacteria to generate the amino acid compositions of community reference proteomes. Taxonomic classifications can be read from the output of the RDP Classifier or from phyloseq-class objects created using the Bioconductor package phyloseq.

The amino acid compositions of community reference proteomes are used to calculate chemical metrics such as carbon oxidation state (Z_C) and stoichiometric hydration state (n_H2O). Lower n_H2O is associated with increasing salinity in samples from the Baltic Sea:

The code to make this plot is from the help page for the plot_metrics function and uses sequence data reported by Herlemann et al. (2016).

Reference proteomes for taxa

Precomputed amino acid compositions of reference proteomes are provided for the Genome Taxonomy Database (GTDB release 207) and the NCBI Reference Sequence Database (RefSeq release 206). See the files in inst/extdata/RefSeq for the steps used to download protein sequences from RefSeq and calculate the total amino acid composition for each NCBI taxonomic ID (taxid). The taxon_AA.R scripts for GTDB and RefSeq were used to generate the reference proteomes for genus- and higher-level archaeal and bacterial taxa (and viruses for RefSeq).

• For 16S rRNA gene sequences classified with a GTDB-based training set (see DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea), taxonomic ranks and names are matched to the GTDB taxonomy to look up reference proteomes.

• For 16S rRNA gene sequences classified using the default training set of the RDP Classifier, chem16S includes manual mapping to the RefSeq taxonomy as described by Dick and Tan (2023).

Installation

After installing phyloseq from Bioconductor, use install_github (provided by either remotes or devtools) to install chem16S from GitHub.

# Install 'BiocManager' from CRAN
if(!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

# Install 'phyloseq' from Bioconductor
BiocManager::install("phyloseq")

# Install 'remotes' from CRAN
if(!require("remotes", quietly = TRUE)) install.packages("remotes")

# Install 'chem16S' from GitHub
remotes::install_github("jedick/chem16S", build_vignettes = TRUE)