diabetes_microbe

Escherichia-Shigella Expansion and metabolite dysregulation in type 3c diabetes: linking microbiome alterations to exocrine pancreatic insufficiency

We compared the gut microbiota of outpatients with T3cDM, type 1 diabetes (T1DM), and healthy controls using 16S rRNA sequencing and community metabolic modelling.

Repository structure

01-tables: Contains initial input files for preprocessing, main downstream analysis and also supplementary analysis. Contains also statistical results.

02-scripts: Contains all the scripts for downstream analysis and producing the figures.

05-results: Contains final figures

The data is available here. https://doi.org/10.5281/zenodo.16794434

Dependencies

Key software and packages used include:

• Nextflow (workflow manager): nf-core/ampliseq v2.12.0
• cutadapt v4.6
• FastQC v0.12.1
• DADA2 v1.30.0
• QIIME2 v2023.7.0
• SILVA v138.1
• R v4.3.0
• python=3.9.4

Python packages mainly used: pandas==1.5.3, seaborn==0.13.2, matplotlib-base=3.8.4, upsetplot==0.9.0. For more details on Python dependencies see diabetes_microbe.yml

For more details on R packages see R_session_info.txt

Data preprocessing

• 16S rRNA amplicon data from DNA. The merged fastq files are stored in zenodo.
• The fastq files are analysed using nf-core/ampliseq v2.12.0

sbatch 02-scripts/nf-core_ampliseq/run_nf_core_ampliseq.slurm

Data anaylsis

Figure 1

• Alpha diversity

02-scripts/Figure1a_alpha_diversity.ipynb
02-scripts/Figure1a_simpson.R

• Beta diversity

02-scripts/Figure1b_beta_diversity.ipynb

• Upset plot

02-scripts/Figure1c_upsetplot.ipynb

• PCA

02-scripts/Figure1d_pca.ipynb

Figure 2

• Compositional analysis

02-scripts/Figure2a_compositional.R

• Core microbiome

02-scripts/Figure2b_core_microbiome_heatmap.R
02-scripts/Figure2c_violin_relative_abundance.R

Figure 3

• Microbial logistic regression model

02-scripts/Figure3abc_logistic_regression_T1DM_T3cDM_CV.R

• Venn diagram

02-scripts/Figure3d_venn_diagram.R

• Genera of interest

02-scripts/Figure3e_violin_relative_abundance_genus.R

Figure 4

• Microbial community metabolic modeling

02-scripts/materials/micom.ipynb
02-scripts/materials/Figure4a_growthrate_boxplot.R
02-scripts/materials/Figure4b_metabolome_barplot_all_taxa.R
02-scripts/materials/Figure4c_metabolome_barplot_eshigella.R

Authors

Erika Kvalem