q2-dbBact

1.1.2
dbBact-based analysis for 16S amplicon experiments. dbBact stores observations about ASVs from over 1000 different experiments. Understand the sources of the bacteria observed in your experiment by using the q2-dbbact plugin statistical tools for term enrichment and wordcloud generation.

source: https://github.com/amnona/q2-dbbact

install guide:

Start your qiime2 conda environment:

conda activate qiime2-XXXX

Install the latest Calour version from github:

pip install "git+https://github.com/biocore/calour.git"

Install the q2-dbBact plugin:

pip install q2-dbbact

q2-dbbact

A Qiime2 plugin for dbBact

See the dbBact paper: Nucleic Acids Research, 2023

Wordcloud enriched barplot heatmap

Features:

  • Differential abundance testing using Calour rank-mean differential abundance test (with dsFDR correction).
  • dbBact term enrichment from differntial abundance results of qiime2 (i.e. songbird/q2-aldex2/ancom/dacomp or the built in rank-mean test).
  • Create a wordcloud of dbBact terms for a given feature table.
  • Generate an interactive heatmap visualization for a feature table. The heatmap provides links to dbBact annotations for each ASV.
  • Generate Venn diagram for a differential abundance result and a given dbBact term.
  • Background dbBact term enrichment analysis for experiments without controls (i.e. what terms are enriched in the bacteria in a given feature table compared to all dbBact experiments of a given type).

Examples:

Run the q2-dbBact enrichment pipeline for a given feature table:

Our input is a feature table and a metadata file with a given column dividing our samples into two groups.

q2-dbBact will detect ASVs different between the two groups, and identify dbBact terms enriched in one of the two groups compared to the other

qiime dbbact enrich-pipeline --i-table cfs-merged.qza --m-metadata-file map.cfs.txt --p-field Subject --output-dir cfs-pipeline

Draw an interactive heatmap

This creates a zoomable heatmap with a list of dbBact annotation for each bacteria that is clicked. Useful for exploring your sequencing results and getting a feeling for what is going on (contaminations, bacterial sources, groups of samples, etc.)

Our input is a feature table and a metadata file with a given column dividing our samples into two groups.

qiime dbbact heatmap --i-table cfs-table.qza --i-repseqs cfs-rep-seqs.qza --i-taxonomy cfs-taxonomy.qza --m-metadata-file map.cfs.txt --p-sort-field Subject --o-visualization heatmap-cfs

heatmap

Draw a dbBact terms wordcloud for the set of bacteria in a feature-table

The wordcloud is created for all the bacteria in the feature table.

The output wordcloud words are dbBact terms associated with the bacteria. The word size corresponds to the F-score (recall and precision) of the term. Blue terms are positively associated (i.e. appear in COMMON/DOMINANT/HIGHER IN annotations) where as red terms (preceeded by a "-") are negatively associated (i.e. appear in LOWER IN annotations).

qiime dbbact draw-wordcloud-vis --i-data cfs-table.qza --i-repseqs cfs-rep-seqs.qza --o-visualization wordcloud-cfs

Wordcloud

Identify differentially abundant bacteria between two sample groups

q2-dbBact utilizes the non-parametric (permutation based) Calour diff_abundance() function. By default it uses a rank-mean test with dsFDR multiple hypothesis correction.

The test can also be performed as a paired test using an additional metadata pair-field (permutations are performed only between samples sharing the same pair-field value).

qiime dbbact diff-abundance --i-table cfs-merged.qza --m-metadata-file map.cfs.txt --p-field Subject --p-alpha 0.1 --p-val1 Patient --p-val2 Control --o-diff diff-cfs-dsfdr

Identify and plot enriched dbBact terms between two groups of bacteria

Performed on the output of a differential-abundance test. q2-dbBact supports the following formats:

This command identifies dbBact terms the are significantly more associated with bacteria from one group compared to the other

qiime dbbact enrichment --i-diff diff-cfs-dsfdr.qza --p-source dsfdr --o-enriched enriched-cfs-dsfdr

The output can be visualized (and the complete table saved) using the visualization command:

qiime dbbact plot-enrichment --i-enriched enriched-cfs-dsfdr.qza --o-visualization barplot-enriched-cfs-dsfdr --p-labels CFS Control

enriched barplot

Venn diagram for examining term distribution in the two groups

Input is the results of a differential abundance analysis (which provides two ASV groups - positive and negative effect size), and a dbBact term.

The venn diagram shows how many of the ASVs in each group have the term, as well as how many total dbBact ASVs have the term associated.

qiime dbbact venn --i-diff diff-cfs-dsfdr.qza --p-terms "small village" --p-source dsfdr --p-label1 Control --p-label2 CFS --o-visualization venn-cfs-human-village

Venn