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Front Microbiol
2019 Jan 01;10:1165. doi: 10.3389/fmicb.2019.01165.
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Genomic and Metagenomic Insights Into the Microbial Community in the Regenerating Intestine of the Sea Cucumber Apostichopus japonicus.
Zhang H
,
Wang Q
,
Liu S
,
Huo D
,
Zhao J
,
Zhang L
,
Zhao Y
,
Sun L
,
Yang H
.
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Host-intestine microbiota interactions have been widely studied in aquatic animals, but these interactions in the intestine regeneration process of the sea cucumber Apostichopus japonicus have been rarely investigated. To understand how intestine regeneration impacts the developing intestinal microbiome composition and function, we performed a case study to characterize the intestinal microbial composition and functional genes of A. japonicus during intestine regeneration stages. High-throughput 16S rRNA gene sequencing revealed significantly different intestine microbiota compositions in different regeneration stages. The phylogenetic diversity and composition of the intestinal microbiota changed significantly in the early regeneration stage and tended to recover in the end stage. During the regeneration process, the abundance of Bacteroidetes and Rhodobacterales increased significantly. A network analysis revealed that Rhodobacteraceae and Flavobacteriaceae may function as keystone taxa in the intestinal microbial community of A. japonicus during intestine regeneration. Metagenomic analyses of representative samples revealed that the microbiomes of regenerating intestines were enriched in genes facilitating cell proliferation, digestion and immunity. The increased abundance of Bacteroidetes elevated the enrichment of genes associated with carbohydrate utilization. Some functional features in the subsystem category changed in a pattern that was consistent with the changing pattern of microbiota composition during intestine regeneration. Our results revealed that seemingly regular alterations in the intestinal microbiome composition and function are associated with intestine regeneration stages. Intestinal microbiota can increase the abundance of beneficial bacterial members and upregulate related functional genes to adapt to intestine regeneration and reconstruct a stable community structure. This study provides a new insight into the mechanism of the host-microbiota interaction response to organ regeneration.
FIGURE 1. Principal component analysis (PCA) based on the relative abundance of 16S rRNA genes from 15 samples (5 sites × 3 replicates per stage). The scatterplot shows principal coordinate 1 (PC1) vs. principal coordinate 2 (PC2). The percentages of variation in the samples described by the plotted PCs are shown on the axes. The 3 replicates for each site are represented by a single color.
FIGURE 2. Composition of bacterial communities in the intestine of the sea cucumber Apostichopus japonicus during different regeneration stages (%). Note: The big pie chart is the class level, the small pie chart is the genus level.
FIGURE 3. Network analysis for connection among bacterial groups in the intestine of the sea cucumber Apostichopus japonicus during the regeneration process. Note: Blue nodes: the high mean degree taxa. The size of the nodes is proportional to the connected degree.
FIGURE 4. Heatmap of the KEGG analysis of intestinal microbiota in samples from different regeneration stages of the sea cucumber.
FIGURE 5. Changes in the functional gene abundance of intestinal microbiota in different regeneration stages.
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