Bacterial composition along the digestive tract of the Horned Screamer (Anhima cornuta), a tropical herbivorous bird

Abstract

Background: The Horned Screamer (Anhima cornuta) is an herbivorous bird that inhabits wetlands of the South American tropical region. We hypothesize that due to its herbivorous niche, its digestive tract compartments may have bacteria specialized in fermenting complex plant carbohydrates. To test this hypothesis, we compared the bacterial communities along the gastrointestinal tract (GIT) of a Horned Screamer captured in Venezuela.

Methods: Samples were taken from tissues and content of the proventriculus and the small intestine (considered for this study as upper GIT), and the large intestine and cecum (lower GIT). The bacterial community was characterized by sequencing the V4 region of the 16S rRNA gene. Bioinformatic analysis was performed using QIIME, QIITA and Microbiome Analyst. The association between microbial taxonomy and function was analyzed using their Greengenes OTU IDs and a custom KEGG BRITE hierarchical tree and visualized with BURRITO.

Results: The Screamer's gastrointestinal microbiota was composed by seven phyla being Firmicutes and Bacteroidetes the most predominant. The dominant taxa in the upper GIT were Helicobacter, Vibrio, Enterobacter, Acinetobacter and Staphylococcus. The dominant taxa in the lower GIT were Oribacterium, Blautia, Roseburia, Ruminococcus, Desulfovibrio, Intestinimonas, Marvinbryantia and Parabacteroides. Complete degradation of cellulose to the end-products acetate, propanoate, butanoate and acetoacetate was found in the upper and lower GIT without significant differences.

Conclusion: Our study confirmed changes in bacterial community composition throughout the GIT of the Horned Screamer primarily associated with the production of metabolic end-products of carbohydrate digestion essential for the fermentation of the herbivorous diet.

Keywords: Cellulose degradation; Herbivore; Microbiota; Tropical bird.

Figure 1. Diagram of the horned screamer gastrointestinal tract (GIT) sections organized as upper GI and lower GI.

Figure 2. Microbiota community diversity comparing upper GI tract samples (crop, proventriculus and small intestine, n = 4) and lower GI tract samples (large intestine and cecum n = 6).

(A) A beta diversity NMDS plot; (B) alpha-diversity plots as boxplots (Chao 1, ACE, Observed and Fisher Index).

Figure 3. Taxonomy profiles at the bacterial communities of the Anhima cornuta gut.

Taxonomy profiles are shown at the phyla (A) and genus levels (B).

Figure 4. Heatmap showing the relative abundance of genus-level taxa according to lower and upper GIT.

Figure 5. Linear discriminant analysis effect size (LEFsE) of bacterial communities.

LEfSe box plot showing phyla-level differences between lower and upper GIT (A) and differences at the genus-level (B). Significantly different taxa are identified with p-values < 0.05 and an asterisk close to the taxa name.

Figure 6. The functional capacity of the upper and lower GIT microbiomes in the Anhima cornuta.

The functional capacity of the upper and lower GIT microbiomes in the fermentation of plant carbohydrates evaluated via the BURRITO framework. (A) Metabolic network of the fermentation of plant carbohydrates composed using KEGG BRITE hierarchical tree and identified KO functional data attributed to the fermentation of plant carbohydrates. (B) The heatmap shows the summary shares of functional attributions for each taxon to each metabolic pathway involved in the fermentation of plant carbohydrates. (C) The heatmap shows the average share of each function attributed to each taxon in each metabolic pathway. Red indicates the highest average share and blue—the lowest. Taxon-function attribution shares were selected based on cut-off <0.01. Abbreviations: PEP, Phosphoenolpyruvate; 3-PG, 3-Phosphoglycerate; 1,3-BisPG, 1,3-Bisphospho-D-glycerate; 2-PG, 2-Phospho-D-glycerate; G6P, Glucose 6-phosphate; F6P, Fructose 6-phosphate; E4P, Erythrose 4-phosphate; X5P, Xylulose 5-phosphate. Each taxon was grouped to correspondent phylum, and taxonomy levels were labeled with asterisks: *—order, **—family, ***—genus, and ****—species.