Avian Gut Microbiome Carbohydrate Fermentation

Taxon-function attributions in the bird’s digestive and intestinal systems related to cellulose and hemicellulose fermentations were analyzed by the BURRITO framework (McNally et al., 2018 (link)). 16S rRNA OTU data were separated into two microbiome datasets: Upper GIT and Lower GIT. Attribution calculations were based on the original PICRUSt and a genomic content table characterized using the Greengenes OTU IDs. The association between taxonomy and function in both microbiome datasets (lower and upper GIT) were evaluated using their Greengenes OTU IDs and a custom KEGG BRITE hierarchical tree, which was composed using KO attributed to cellulose and hemicellulose metabolism, including starch and sucrose metabolism, galactose metabolism, glycolysis, pentose phosphate pathway, pyruvate, butanoate and propanoate metabolism. The summary levels of functional attributions for each taxon to each metabolic pathway involved in the fermentation of plant carbohydrates and average shares of each function attributed to each taxon were presented as a heatmap constructed using GraphPad Prism version 9 (GraphPad Software, San Diego, CA, USA). Metabolic network of the fermentation of plant carbohydrates were composed using KEGG BRITE hierarchical tree (Kanehisa & Goto, 2000 (link)) and identified KO functional data attributed to the fermentation of plant carbohydrates. The network was constructed using Cytoscape (Shannon et al., 2003 (link)).