Figure 1.
UPGMA clustering over Sørensen similarity of gut microbiota composition between transgenic fish and wild-type controls across different developmental stages.
The similarity matrix was calculated using the binary data, and clustering was performed using the unweighted pair-group method with arithmetic average (UPGMA). Ti and Ci indicate the ith replication of transgenic fish and wild-type control, respectively; Tfi, Tmi, and Thi represent the ith foregut, midgut, and hindgut samples from transgenic fish, respectively, and Cfi, Cmi, and Chi from the corresponding part of controls; Ts and Tw represent the sediment and water samples collected from the pond where transgenic fish were reared, and Cs and Cw represent controls; F indicates food sample.
Figure 2.
Comparison of similarities and differences for gut microbiota composition between transgenic fish and wild-type controls across different developmental stages.
(a) Comparison of the average Sørensen index obtained from DGGE patterns of 16S rRNA genes between transgenic fish and wild-type controls or within each group of transgenic fish and wild-type controls. (b) Comparison of Raup and Crick similarity index (SRC) obtained from DGGE patterns of 16S rRNA genes between transgenic fish and wild-type controls or within each group of transgenic fish and wild-type controls. Dashed lines indicate significant cutoff for difference (low line) and similarity (upper line). Error bars represent the standard error of the mean.
Figure 3.
Principal Component Analysis (PCA plot with UniFrac scaled axis) of individual samples with different diet treatments.
For each sample code, the first letter T represents transgenic fish, and C wild-type controls; the middle letter(s) indicates the diet treatments (C: control diet, HP: high protein diet, HC: high carbohydrate diet, HL: high lipid diet), and the last numbers represent replicate samples.
Table 1.
Alpha-diversity of gut microbiota calculated according to the composition and relative abundance of OTUs with 97%-identity.
Figure 4.
Comparison of relative Bacteroidetes and Firmicutes abundance at different developmental stages.
Real-time quantitative PCR (Q-PCR) was used to quantify the abundance of gut Firmicutes and Bacteroidetes based on the 16S rRNA genes (V3 region). (a) Relative abundance of Firmicutes and Bacteroidetes in transgenic fish. (b) Relative abundance of Firmicutes and Bacteroidetes in wild-type controls.
Figure 5.
Triplot of the redundancy analysis (RDA) showing significant relationship between metabolic-related factors (response variables) and microbial groups (explanatory variables).
First and second ordination axes were plotted, representing 22.6% and 7.9% of the variability in the data set, respectively. P-values obtained by Monte Carlo test were reported. For each sample code, the first letter T represents transgenic fish, and C wild-type controls; the middle letter(s) indicates the diet treatments (C: control diet, HP: high protein diet, HC: high carbohydrate diet, HL: high lipid diet), and the last numbers represent replicated samples. GLU represents glucose, AST aspartate aminotransferase, and HDL high-density lipoprotein.
Table 2.
Summary statistics of redundancy analysis (RDA) showing the relationships between gut microbiota and host metabolism by canonical axes with associated p values from Monte Carlo test.
Figure 6.
Histological analyses of liver tissues. Liver tissues from 4 different diet treatments were formaldehyde-fixed, followed by staining with Hematoxylin and eosin.
The results (75×) from transgenic fish are shown in the upper panels, and wild-type controls with corresponding diet treatments in the lower panels. Arrows in upper panels indicate lipid droplet (blue) and those in lower panels (green) show glycogen deposits.
Table 3.
Comparison of metabolic differences between transgenic and wild-type fish.