3.6 | LEfSe analysis of significantly enriched microbial communities
Linear discriminant analysis effect size (LEfSe) was used to characterize enriched microbial communities (Figure 6A). There were 48 differences among the four fish species with different feeding habits, classified from phylum to genus. The Proteobacteria phylum was common to all the four fish species. The omnivorous species had significantly higher enriched gut microbiota species than the other three species. Indeed, omnivorous species had significantly enriched Fusobacteria, Actinobacteria and Verrucomicrobia phyla compared to carnivorous, herbivorous and filter-feeder fish species. The most enriched bacteria in the gut of the four fish species followed the trend omnivorous (25) > carnivorous (10) > filter-feeder (8) > herbivorous (5) (Figure 6B). The omnivorous species enriched Fusobacteriales, Fusobacteriaceae, Fusobacteriia, Fusobacteria, Dechloromonas, Saprospirales, Saprospirae, Chitinophagaceae, Paucibacter, Microbacteriaceae, Luteolibacter, Clavibacter, Actinomycetales, Actinobacteria, Actinobacteria, Zymomonas, Verrucomicrobiales, Verrucomicrobiae, Verrucomicrobia, Verrucomicrobiaceae, Rhodobacter, Rhodobacterales andRhodobacteraceae . The herbivorous fish species enrichedAeromonadales, Aeromonadaceae, Lachnospiraceae, Clostridia andClostridiales . Moreover, carnivorous fish species enrichedAcinetobacter, Moraxellaceae, Hyphomonadaceae, Mycoplana, Pseudomonas, Pseudomonadaceae, Pseudomonadales, Caulobacteraceae, Caulobacterales and Proteobacteria . The filter-feeder fish enriched Anaerolineae, Neisseriales, Neisseriaceae, Escherichia, Comamonadaceae, Burkholderiales, Betaproteobacteria andLimnobacter .
3.7 | Predicted gut microflora functions
A total of 423 metabolism pathways (Kyoto Encyclopedia of Genes and Genomes, KEGG level-3) were constructed. The four fish species showed marked differences in functional profile (Supplementary Figure 3S). The microbial functions among the four fishes with different feeding habits showed that, 39 pathways related to digestion were identified, including those associated with carbohydrate, protein and amino acid, energy and lipid metabolism (Figure 7). Of all the pathways identified, 27 pathways were significantly changed (Figure 7). The herbivorous fish species had higher carbohydrate metabolism than carnivorous fish species (p< .05). Moreover, herbivorous fish species increased pathways related to carbohydrate metabolism [i.e. glycolysis III (from glucose), galactose degradation I (Leloir pathway), superpathway of D-glucarate and D-galactarate degradation, reductive TCA cycle I and incomplete reductive TCA cycle] than in carnivorous fish species. Interestingly, carnivorous had more enriched protein and amino acid metabolism pathways [superpathway of ornithine degradation, superpathway of L-arginine and L-ornithine degradation and L-arginine degradation II (AST pathway)] and lipid metabolism (fatty acid salvage) than herbivorous and omnivorous fish species.