This code is associated with the paper from Di Rienzi et al., "Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids". eLife, 2018. http://dx.doi.org/10.7554/eLife.32581

#Lactobacillus_soybeanoil

#The files in this repository are the qiime, R, perl, and other bash commands utilized to process the data in the project, "Resilience of small intestinal lactobacilli to the toxicity of soybean oil fatty acids"

mappingfile.txt

provides the metadata for all mice microbiome samples

biomedit.pl

perl script used in the creation of Figure 4 – Figure supplement 2D

QiimeandRcommands.txt

Qiime and R commands for Figures 4-2A,B,D, 4-3, 4C,D, 4-2, 4B

weighteddistancemetricpairs.pl

perl script used in the creation of Figure 4B

linoleicacid_threetimepointratio.R

R commands for Figures 4E, 4–4, 2, 2-1A,B

linoleicacidgrowthdata.txt

raw data for Figures 2 and

note that missing metadata for the JW strains are filled in during the creation of the Figure using the information in JWstraininfo.txt

JWstraininfo.txt

provides the information on the L. reuteri strains isolated from a variety of animals

used in the creation of Figure 2

LactoGenomeAssembly.txt

pipeline using spades, Bandage, and nucmer to assemble the parental strains (LR0 and LJO)

GATK.txt

BWA-MEM, Picard, and GATK pipelines for identifying mutations in the strains and populations for evolved Lactobacilli