BRB2024

The BRB project data analysis

Amplicon

The analysis of the 16S rRNA gene sequencing of the mouse oral and cecal samples.

• BRB_amplicon_CAPR.Rmd: R Markdown document of the 16S rRNA gene sequencing analysis.
• BRB_amplicon_CAPR.html: HTML report of the 16S rRNA gene sequencing analysis.
• asv_tax.xlsx: The taxonomy assignment of the ASVs.
• cecum_asv_table.xlsx: The ASV table of the 20 cecal samples.
• cecum_a_diversity.xlsx: The ASV richness of the cecal samples.
• cecum_metadata.xlsx: The metadata for the cecal samples.
• cecum_Family.xlsx: The family abundance table of the cecal samples.
• cecum_akker.xlsx: The clr abundance of A. muciniphila in the cecal samples.
• cecum_DMSO_BRB_table.xlsx: The ASV table of the cecal samples in DMSO and BRB groups.
• cecum_DMSO_BRB_metadata.xlsx: The metadata for the cecal samples in DMSO and BRB groups.
• cecum_glm_table.xlsx: The ASV table of the cecal samples in DMSO, DBP, BRB, and BRB+DBP groups.
• cecum_glm_metadata.xlsx: The metadata for the cecal samples in DMSO, DBP, BRB, and BRB+DBP groups.
• saliva_asv_table.xlsx: The ASV table of the 20 oral samples.
• saliva_a_diversity.xlsx: The ASV richness of the oral samples.
• saliva_metadata.xlsx: The metadata for the oral samples.
• saliva_Family.xlsx: The family abundance table of the oral samples.
• saliva_akker.xlsx: The clr abundance of A. muciniphila in the oral samples.
• saliva_enter.xlsx: The clr abundance of Enterococcus_E in the oral samples.
• saliva_DMSO_BRB_table.xlsx: The ASV table of the oral samples in DMSO and BRB groups.
• saliva_DMSO_BRB_metadata.xlsx: The metadata for the oral samples in DMSO and BRB groups.
• ASV_richness.xlsx: The ASV richness of both oral and cecal samples

Strain

The in vitro analysis of the strain screening with BRB and DBP treatment.

• BRB_Strain_CAPR.Rmd: R Markdown document of the in vitro strain screening assay.
• BRB_Strain_CAPR.html: HTML report of the in vitro strain screening assay.
• JEB00020.xlsx: The OD values of strain A. muciniphila JEB00020 treated by BRB and DBP over 72 hours.
• JEB00423.xlsx: The OD values of strain A. muciniphila JEB00423 treated by BRB and DBP over 72 hours.
• BRB.xlsx: The growth curve parameters of our lab strains treated after BRB treatment.
• DBP.xlsx: The growth curve parameters of our lab strains treated after DBP treatment.
• GTDB_taxonomy.xlsx: The taxonomy assignment of the lab strains.
• Bisanz_strain.xlsx: The species names of the lab strains.
• RAxML_bestTree.faas_refined.tre: The constructed tree of the lab strains with the RAxML plugin.