Integrated Bacterial and Fungal Diversity Analysis Reveals the Gut Microbial Alterations in Diarrheic Giraffes

Abstract

Gut microbiota has been demonstrated to be associated with multiple gastrointestinal diseases, but information regarding the gut microbial alternations in diarrheic giraffe remains scarce. Here, 16S rDNA and ITS gene amplicon sequencing were conducted to investigate the gut microbial composition and variability in diarrheic giraffes. Results demonstrated that Firmicutes and Proteobacteria were the most dominant phyla in the gut bacterial community, whereas Ascomycota and Basidiomycota were observed to be predominant in the gut fungal community regardless of health status. However, the species and relative abundance of preponderant bacterial and fungal genera in healthy and diarrheic giraffes were different. In contrast to the relatively stabilized gut fungal community, gut bacterial community displayed a significant decrease in the alpha diversity, accompanied by distinct changes in taxonomic compositions. Bacterial taxonomic analysis revealed that the relative abundances of eight phyla and 12 genera obviously increased, whereas the relative abundances of two phyla and eight genera dramatically decreased during diarrhea. Moreover, the relative richness of five fungal genera significantly increased, whereas the relative richness of seven fungal genera significantly declined in diarrheic giraffes. Taken together, this study demonstrated that diarrhea could cause significant alternations in the gut microbial composition of giraffes, and the changes in the gut bacterial community were more significant than those in the gut fungal community. Additionally, investigating the gut microbial characteristics of giraffes in different health states is beneficial to provide a theoretical basis for establishing a prevention and treatment system for diarrhea from the gut microbial perspective.

Keywords: 16S rDNA; ITS; diarrhea; giraffe; gut microbiota.

FIGURE 1

Gut bacterial and fungal OTU distribution and feasibility analysis. (A–C) Venn diagrams for gut bacterial OTU distribution. (D–F) Bacterial rarefaction and rank abundance curves were used for assessing the quality of sequencing including depth, abundance, and evenness. (G–I) Venn diagrams for gut fungal OTU distribution. (J–L) Fungal rarefaction and rank abundance curves were used to evaluate the quality of sequencing including depth, abundance, and evenness. Each colored curve displayed in the figures represents a sample.

FIGURE 2

The alternations of gut bacterial and fungal diversities during diarrhea. Gut bacterial and fungal alpha diversities can be evaluated by Good’s coverage (A,E), ACE (B,F), Simpson (C,G), and Shannon (D,H). (I,J) Principal coordinate (PCoA) analysis based on the weighted and unweighted UniFrac distance of gut bacterial community. (L,M) Principal coordinate (PCoA) analysis of gut fungal community. (K,N) Gut bacterial and fungal clustering analysis based on unweighted pair-group method with arithmetic means (UPGMA). All of the data represent means ± SD. **p < 0.01.

FIGURE 3

The composition and relative abundance of the gut microbial community at the phylum and genus levels. (A,B) The gut bacterial relative abundance and composition of healthy and diarrheic giraffes at the phylum and genus levels. (C,D) The gut fungal relative abundance and composition of healthy and diarrheic giraffes at the phylum and genus levels. (E,F) Heatmap of the 50 most abundant gut bacterial and fungal genera in healthy and diarrheic giraffes.

FIGURE 4

Significant alternations in the gut bacterial abundance at the level of phylum (A) and genus (B) during diarrhea. All of the data represent means ± SD. *p < 0.05; **p < 0.01; ***p < 0.001 and ****p < 0.0001.

FIGURE 5

LEfSe analysis integrated with LDA scores revealed differential biomarkers associated with diarrhea in giraffes. (A,C) Cladogram revealing the phylogenetic distribution of intestinal bacteria and fungus correlated with the control or diarrheic groups. (B,D) The differences in the relative abundance of bacteria and fungi between the control and the diarrheic groups. LDA scores > 4 was considered statistically significant.

FIGURE 6

Significant changes in the gut fungal abundance at the level of phylum and genus during diarrhea. *p < 0.05; **p < 0.01 and ***p < 0.001 represent distinct difference between control and diarrheic groups.

FIGURE 7

Correlation network reveals the correlation among the different bacterial (A) and fungal (B) genera. The circles with different colors indicate the name of bacterial and fungal genus, and their sizes represent relative abundance. The strength of the correlation between both genera is positively related to the thickness of the line. The green line between both genera represents a positive correlation, whereas the orange line indicates a negative correlation.