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.