Diversification of animal gut microbes and NRPS gene clusters in some carnivores, herbivores and omnivores

Figures & data

Table 1. Description of the 24 faecal samples from different herbivores, carnivores and omnivores used in this study.

Sample group	Code of sample
Herbivorous mammal (A group)
Elephas maximus Linnaeus	A1 A2 A3
Cervus nippon	B1 B2 B3
Tragelaphus oryx	C1 C2 C3
Carnivorous mammal (B group)
Panthera tigris Amoyensis	D1 D2 D3
Panthera leo	E1 E2 E3
Vulpes vulpes fulva	F1 F2 F3
Omnivorous bird (C group)
Pavo cristatus	G1 G2 G3
Struthio camelus	H1 H2 H3

Figure 1. Faecal bacterial community at the phylum (a) and genus (b) level. (a and b) Relative abundance of bacteria in the 24 faecal samples from different herbivores, carnivores and omnivores. Phyla or genera with abundance of less than 1% abundance were merged into ‘others’. The letters A to H followed by a number indicate the samples; A–C, herbivores; D–F, carnivores; G–H, omnivores (see Table 1).

Figure 2. Statistical comparison of the relative abundance (a and b) and bacterial diversities (c and d) of gut microbiota among the three groups. (a) Comparison of dominant phyla in the A, B and C groups. (b) Comparison of dominant genera in the A, B and C groups. (c) Bacterial community richness (measured by ACE index) in the A, B and C groups. (d) Bacterial community diversity (measured by Sobs index) in the A, B and C groups. Differences were considered statistically significant at *p < 0.05; **p < 0.01; ***p < 0.001 level. Groups: A, herbivores; B, carnivores; C, omnivores.

Figure 3. Relationship of the gut microbiota from different herbivores, carnivores and omnivores. (a) Clustering tree of the gut microbiotas in different animals from herbivores (A group), carnivores (B group) and omnivores (C group). Gut microbiota trees were generated using the UPGMA (unweighted pair group method with arithmetic mean) algorithm based on the Bray-Curtis distances generated by Mothur. (b) Principal coordinate analysis (PcoA) of community structure of the gut microbiotas of the three groups. Circular (red), triangular (blue) and diamond (green) shapes represent the gut microbiotas from herbivores (A group), carnivores (B group) and omnivores (C group), respectively. Distances between symbols on the ordination plot reflect relative dissimilarities in community structures. (c) Network-based analysis of faecal microbial communities in herbivores, carnivores and omnivores.

Figure 4. Richness and relationship of NRPS gene clusters in gut microbiome. (a) Relative abundance of predicted substrate of NRPS domains in the gut microbiome from different herbivores, carnivores and omnivores. (b) Principal coordinate analysis (PcoA) of community structure of the NRPS gene clusters in the three groups. Circular, triangular and square shapes represent the domains of NRPS in the gut microbiome from herbivores (A group), carnivores (B group) and omnivores (C group), respectively. Distances between symbols on the ordination plot reflect relative dissimilarities in community structures. (c) Bray-Curtis distances tree of the evolution of the NRPS gene domains in different herbivores (A group), carnivores (B group) and omnivores (C group).

Data availability

The raw 16S rRNA sequences supporting the results of this study are available in the GenBank Database under the accession number PRJNA631813.