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PeerJ
2020 Jan 01;8:e10260. doi: 10.7717/peerj.10260.
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Tracking the dynamics of individual gut microbiome of sea cucumber Apostichopus japonicus during gut regeneration.
Yamazaki Y
,
Sakai Y
,
Yu J
,
Mino S
,
Sawabe T
.
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Sea cucumbers possess the remarkable capacity to regenerate their body parts or organs. Regeneration of host organs and/or body parts involves reconstruction of the host associated microbiota, however, the dynamics and contribution of microbiota to the regeneration process are largely unknown due to a lack of experimental models. To track the dynamics of individual gut microbiomes during gut regeneration, both caged mariculture and laboratory isolator systems of sea cucumbers (Apostichopus japonicus) were developed and longitudinal meta16S analyses were performed. Under natural environmental conditions in the caged mariculture system, both bacterial and eukaryotic communities in sea cucumbers' guts appeared to be reconstructed within 4 months after evisceration. Using the laboratory isolator, which can trace daily dynamics, we found that fecal microbiota collected before evisceration were clearly different from those collected after evisceration. We also identified eight key bacteria, belonging to Alteromonadaceae, Rhodobacteraceae, Oceanospirillaceae and family-unassigned Gammaproteobacteria, suggesting that these bacteria might interact with the host during the gut regeneration process. Six of the eight key bacteria were isolated for further bioassay using the isolator developed in this study to test whether these isolates affect gut regeneration.
Figure 1. Unweighted UniFrac analyses in the caged mariculture experiment.Red and blue colored symbols show gut-regenerated and control groups, respectively. Star-shaped symbols represent samples collected in December, when the gut of sea cucumber was removed. Closed circle, open circle, cone, and diamond-shaped symbols represent samples collected in April, May, June, and July, respectively. (A) Bacterial communities, and (B) eukaryotic communities. December samples were excluded due to limited number of eukaryotic reads.
Figure 2. Unweighted UniFrac distance-based 2D PCoA in the laboratory isolator.Specimens in the regeneration group are indicated by “Regen-” with red, green, blue, purple, and orange circle depend on individual. In the gut-regenerated individual, dark to shaded gradation in each color symbol indicates temporal scale after gut-regeneration. Specimens in the control group are indicated by “Cont-” with gray scale. Star indicates samples collected before evisceration.
Figure 3. Bacterial community dynamics at family level in the laboratory isolator.The top 10 families are shown in the bar plot. Minor taxa and unassigned reads are clustered into others. Upper numbers are time points corresponding to Fig. S2.
Figure 4. Dendrogram-connected heatmaps features in the laboratory isolator.Difference of relative abundance of features with >500 reads between time-point zero and time-point 17 was calculated. The heat maps show four individuals from the regeneration group and three individuals from the control group, and specimen “Regen-2” was excluded due to limited number of samples. More vivid magenta corresponds to more abundant OTUs in time-point 17 than in time-point 0, and more vivid cyan corresponds to more abundant OTUs in time-point 0 than in time-point 17. Features are placed on a maximum-likelihood tree on the basis of representative reads of each feature. The color bar shows family level affiliation of each feature. Unassigned and minor taxa are combined into others. Red stars indicate key features whose relative abundance increased after evisceration in the regeneration group.
Figure 5. Dynamics of relative abundance of key features.Eight key features are shown in (A–H), respectively. * indicates statistically significant (p < 0.05) compared to control group. Gut-regenerated individuals no. 1, 3, 4 and 5 are indicated by red-closed square, aqua blue-closed circle, purple-closed diamond, and brown-closed triangle, respectively. Control group no. 1 to 3 are indicated by light-gray open square, gray open circle, and black open triangle, respectively.
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