16S profiling analysis

.gitattributes

@@ -15,3 +15,5 @@ assays/MicrobiotaReconstitutionFlowpot/dataset/.gitkeep filter=lfs diff=lfs merg
 assays/Mono-association[[:space:]]experiment[[:space:]]of[[:space:]]R401[[:space:]]on[[:space:]]Athaliana[[:space:]]seedlings[[:space:]]in[[:space:]]agar[[:space:]]plates/dataset/.gitkeep filter=lfs diff=lfs merge=lfs -text
 assays/DNA[[:space:]]Isolation/dataset/.gitkeep filter=lfs diff=lfs merge=lfs -text
 assays/Library[[:space:]]preparation[[:space:]]for[[:space:]]bacterial[[:space:]]16S[[:space:]]rRNA[[:space:]]gene[[:space:]]profiling/dataset/.gitkeep filter=lfs diff=lfs merge=lfs -text
+assays/Analysis[[:space:]]of[[:space:]]16S[[:space:]]profiling/dataset/.gitkeep filter=lfs diff=lfs merge=lfs -text
+assays/Analysis[[:space:]]of[[:space:]]16S[[:space:]]profiling/dataset/ComProfiling.jpg filter=lfs diff=lfs merge=lfs -text

assays/Analysis of 16S profiling/protocols/16SProfilingAnalysis.md

+## Analysis of 16S profiling data
+
+### ASV table generation
+
+Amplicon sequencing reads from *A. thaliana* roots and Flowpot soil were quality filtered and demultiplexed according to their barcode sequence using QIIME (26) and unique amplicon sequencing variants (ASVs) were inferred from error-corrected reads, followed by chimera filtering. ASVs were mapped to the reference 16S rRNA sequences (downloaded from “www.at-sphere.com”) to generate an ASV count table. All steps were carried out using the Rbec R package (27). Analysis was performed on samples with a sequencing depth of at least 500 high-quality reads.
+
+
+### Alpha- and beta-diversity
+
+Analyses and visualization were performed in the R statistical environment (Version 4.1.2).
+Alpha and beta diversity were calculated on non-rarefied ASV count tables (28). Alpha-diversity (Shannon index) was calculated with the “plot_richness” function in phyloseq package (29).
+Beta-diversity (Bray-Curtis dissimilarities) was calculated using the “ordinate” function in phyloseq package and used for unconstrained ordination by Principal Coordinate Analysis (PCoA). Statistical significances were assessed using permutational multi-variate analysis of variance (PERMANOVA) using the adonis function in the vegan package.