Gut microbiomes of cyprinid fish exhibit host-species symbiosis along gut trait and diet

Abstract

Teleost omnivorous fish that coexist partially sharing resources are likely to modify their gut traits and microbiome as a feedback mechanism between ecological processes and evolution. However, we do not understand how the core gut microbiome supports the metabolic capacity of the host and regulates digestive functions in specialized omnivorous fish gut traits. Therefore, we evaluated the gut microbiome of eight omnivorous fish from a single family (i.e., Cyprinidae) in the current study. We examined the correlation between host phylogeny, diet composition, and intestinal morphological traits related to the intestinal microbiome. The results indicated that cyprinid fish with similar relative gut lengths had considerable gut microbiome similarity. Notably, the SL (short relative gut length) group, as zoobenthos and zooplankton specialists, was abundant in Proteobacteria and was less abundant in Firmicutes than in the ML (medium relative gut length) and LL (long relative gut length) groups. These fish could extract nutrients from aquatic plants and algae. Additionally, we found the relative abundance of Clostridium and Romboutsia to be positively correlated with host relative gut length but negatively correlated with the relative abundance of Cetobacterium, Plesiomonas, Bacteroides, and Lactobacillus, and host-relative gut length. We also show a positive linear relationship between host gut microbiome carbohydrate metabolism and relative gut length, while the amino acid and lipid metabolism of the gut microbiome was negatively correlated with host-relative gut length. In addition, omnivorous species competing for resources improve their ecological adaptability through the specialization of gut length, which is closely related to variation in the synergy of the gut microbiome. Above all, specialized gut microbiota and associated gut morphologies enable fish to variably tolerate resource fluctuation and improve the utilization efficiency of nutrient extraction from challenging food resources.

Keywords: Cyprinidae; coexistence; gut length; gut microbiome; metabolism.

FIGURE 1

Location of the sample sites.

FIGURE 2

An overview of the data. (A) A circos chart indicating microbial communities in fish gut samples at the phylum level. The inner circular diagram shows the relative abundance of different phyla in different cyprinid fish gut samples. Only those with mean relative abundance more than 1% for phylum are shown. Sequences that could not be assigned at the phylum level were marked as “Unclassified”; (B) hierarchical clustering of gut microbiome of the different cyprinid fish based on Bray-Curtis distance; (C) phylogenetical clustering based on host genetic distance (the CO1 gene); (D) relationship between fish gut microbiome dissimilarity based on Bray-Curtis distance and host genetic distance (the CO1 gene). BA, Black Amur bream; BC, Barbel chub; CA, Common carp; GC, Grass carp; MC, Mud carp; SC, Silver carp; TC, Topmouth culter; XD, Bleeker’s yellow tail.

FIGURE 3

Alpha diversity results of the gut microbial community pertaining for the eight different fish species at three relative gut length levels. The Shannon (A) and Ace (C) index of gut microbiota composition from the eight different fish species at three relative gut length levels. Samples marked different lowercase letters indicate significant differences (a > b > c; p < 0.05) among different fish species. Linear regression of the Shannon (B) and Ace (D) index among eight cyprinid fish species vs. mean of their relative gut length with 95% confidence interval. BA, Black Amur bream; BC, Barbel chub; CA, Common carp; GC, Grass carp; MC, Mud carp; SC, Silver carp; TC, Topmouth culter; XD, Bleeker’s yellow tail; RGL, Relative gut length; SI, Shannon index; AI, Ace index.

FIGURE 4

An overview of the data. (A) NMDS (non-metric multidimensional scaling) based on bray curtis distance matrix, demonstrating different fish samples. Significance tests of the bacterial community composition with analysis of similarities (ANOSIMm), indicating the significance of defined species based on Bray-Curtis distance. The individual samples are color-coordinated according to the different species. (B) Pearson correlation analysis between relative gut length and dominant phylum in the eight fish species *p < 0.05; **p < 0.01; ***p < 0.001. BA, Black Amur bream; BC, Barbel chub; CA, Common carp; GC, Grass carp; MC, Mud carp; SC, Silver carp; TC, Topmouth culter; XD, Bleeker’s yellow tail.

FIGURE 5

Comparison of the bacterial community in the different relative gut length groups. Dominant gut microbiota composition in the different groups at the phylum (A) and order (B) level; each bar represents average relative abundance of each bacterial taxon within a group at the phylum and order level. BA, Black Amur bream; BC, Barbel chub; CA, Common carp; GC, Grass carp; MC, Mud carp; SC, Silver carp; TC, Topmouth culter; XD, Bleeker’s yellow tail.

FIGURE 6

An overview of the data. (A) NMDS based on the bray curtis distance matrix demonstrating different fish samples at the phylum and order level. The individual sample is color-coordinated according to the different gut length groups; significance tests of the bacterial community composition with analysis of similarities (ANOSIM), indicating the significance of groups based on Bray-Curtis distances. (B) The Venn diagram illustrating the shared and unique phylum and orders in the different gut length groups. (C) One-way ANOVA analysis demonstrating significant differences of gut bacterial phyla and order in the different gut length groups. Samples marked by an asterisk indicate significant differences (*p < 0.05; ^**p < 0.01) among relative gut length groups.

FIGURE 7

Linear regression of relative abundance of gut core microbiome (the genera level) among eight cyprinid fish species vs. mean of their relative gut length, with 95% confidence interval. (A) Cetobacterium; (B) clostridium; (C) plesiomonas; (D) romboutsia; (E) bacteroides; (F) lactobacillus. RGL, Relative gut length; RB, Relative abundance; Cet, Cetobacterium; Clo, Clostridium; Ple, Plesiomonas; Rom, Romboutsia; Bac, Bacteroides; Lac, Lactobacillus.

FIGURE 8

KEGG categories derived from the 16S rRNA sequences of the fish gut microbiomes by PICRUSt. (A) PCoA of the binary Jaccard dissimilarity of the functional profiles (Level 3). (B) The Heatmap presenting the relative abundance of digestion-related bacterial gene functions among the three gut length groups. Samples marked different capital letters indicate significant differences (A > B > C; p < 0.05) among relative gut length groups. (C) Linear regression of relative abundance of digestion-related bacterial gene functions among eight Cyprinidae fish species vs. mean of their relative gut length, with 95% confidence interval.