New perspectives on an old grouping: the genomic and phenotypic variability of Oxalobacter formigenes and the implications for calcium oxalate stone prevention
Scripts to reproduce the analyses in "New perspectives on an old grouping: the genomic and phenotypic variability of Oxalobacter formigenes and the implications for calcium oxalate stone prevention"
01_custom_dada2_script.R: DADA2 pipeline for reads resulting from the custom demultiplexing script
02_filtering.R: filters out low-abundance and rare ASVs + low-depth samples
03_decontam.R: script for the decontam pipeline
04_adonis.R: script for Adonis2 (PERMANOVA) analysis
05_ancom_asv.R: script to run ANCOM
06_maaslin2_asv.R: script to run MaAsLin2
07_differential_abundance_fig.R: script to generate differential abudance plot for Figure 5
08_picrust2.R: runs PICRUSt2 for metabolic inferencing
09_barplots.R: generates bar plots on Figure 5
10_PCA.R: generates PCA in Figure 5
01_Figure1.R: generates Figure 1
02_Figure2.R: generates Figure 2
03_Figure3.R: generates Figure 3
RUCS_primer_filter.R: scripts to filter primers from RUCS
oxalobacter_genome_analysis.txt: scripts for main genome analysis
To use these scripts, please download the demultiplexed reads from the Sequence Read Archive (PRJNA836912) and/or the genomes from GenBank (PRJNA841018).
Type strains can be found at the following culutre collection centers.
O. formigenes OxBT --> ATCC 35274
O. aliiformigenes Va3T --> TSD-348, DSM 115068
O. paeniformigenes OxGP1T --> TSD-347, DSM 115066
O. paraformigenes HOxBLST --> TSD-346, DSM 115067
O. vibrioformis WoOx3T --> DSM 5502
Chmiel JA, Carr C, Stuivenberg GA, Venema R, Chanyi RM, Al KF, Giguere D, Say H, Akouris PP, Domínguez Romero SA, Kwong A, Tai V, Koval SF, Razvi H, Bjazevic J, Burton JP (2022) New perspectives on an old grouping: the genomic and phenotypic variability of Oxalobacter formigenes and the implications for calcium oxalate stone prevention. Front. Microbiol. 13:1011102. doi: 10.3389/fmicb.2022.1011102