Additional file 12 of Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure
Creators: name: Zou, Angela
name: Nadeau, Kerry
name: Xiong, Xuejian
name: Wang, Pauline W.
name: Copeland, Julia K.
name: Lee, Jee Yeon
name: Pierre, James St.
name: Ty, Maxine
name: Taj, Billy
name: Brumell, John H.
name: Guttman, David S.
name: Sharif, Shayan
name: Korver, Doug
name: Parkinson, John
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 12: Supplemental Figure 12. Comparison of changes in pathway-specific gene expression, with changes in taxon abundance and global gene expression for three select pathways. For each pathway (glycolysis, purine metabolism and cell wall biogenesis) we calculate the shift in expression across the four conditions tested (i.e. corn + AGPs v corn; wheat + AGPs v wheat; corn v wheat; and corn + AGPs v wheat + AGPs). The absolute deviation of these changes in pathway-specific expression were then calculated relative to: 1) the relative change in abundance of that taxon (as measured by the log2 fold-change associated with that taxon according to 16S rDNA-based relative abundance); and 2) the total change in RNA for that taxon (as measured by the log2 fold-change in total taxon RNA, calculated by summing RPKM values for all genes for that taxon). Here OTUs are grouped into genera. In the box-plots, taxa with values close to zero, indicate that the shift in pathway gene expression was driven by a general shift in either taxon abundance (16S) and/or global taxon expression. Of the 48 comparisons presented, 42 show that at least 60% of taxa with pathway expression, deviate by greater than a log2 fold change from changes in relative abundance (as measured by 16S rDNA) or global taxon expression (as measured by total taxon RPKM). Note, due to lack of phylogenetic resolution associated with the 16S rDNA datasets, these comparisons feature fewer taxa than the comparisons involving taxon-specific global gene-expression. Single sample Wilcoxon tests further reveal that for 43 of the datasets, pathway-specific gene-expression significantly deviates from either taxon-abundance or global gene expression (* p&lt;0.05; ** p&lt; 0.01; *** p&lt;0.001). The lower panels show the 20 genera exhibiting the greatest divergence in pathway expression relative to global gene expression. For the Corn v Corn+AGP comparison for the glycolysis pathway, we identified ‘Other Bacteria’ and various Proteobacterial groups as possessing the greatest deviation between pathway-specific and global fold change expression. For the Wheat v Wheat+AGP comparison. among the taxa with the greatest deviation between pathway-specific and global fold change expression, were taxa classified as ‘Other Bacteria’, ‘Peptostreptococcaceae’ and ‘Clostridiaceae’.