ECB-ART-43477PLoS One January 1, 2014; 9 (6): e100092.
Bacterial community composition in the gut content and ambient sediment of sea cucumber Apostichopus japonicus revealed by 16S rRNA gene pyrosequencing.
The composition of the bacterial communities in the contents of the foregut and hindgut of the sea cucumber Apostichopus japonicus and in the ambient surface sediment was surveyed by 16S rRNA gene 454-pyrosequencing. A total of 188,623 optimized reads and 15,527 operational taxonomic units (OTUs) were obtained from the ten gut contents samples and four surface sediment samples. The sequences in the sediments, foregut contents, and hindgut contents were assigned to 38.0±4.7, 31.2±6.2 and 27.8±6.5 phyla, respectively. The bacterial richness and Shannon diversity index were both higher in the ambient sediments than in the gut contents. Proteobacteria was the predominant phylum in both the gut contents and sediment samples. The predominant classes in the foregut, hindgut, and ambient sediment were Holophagae and Gammaproteobacteria, Deltaproteobacteria and Gammaproteobacteria, and Gammaproteobacteria and Deltaproteobacteria, respectively. The potential probiotics, including sequences related to Bacillus, lactic acid bacteria (Lactobacillus, Lactococcus, and Streptococcus) and Pseudomonas were detected in the gut of A. japonicus. Principle component analysis and heatmap figure showed that the foregut, hindgut, and ambient sediment respectively harbored different characteristic bacterial communities. Selective feeding of A. japonicus may be the primary source of the different bacterial communities between the foregut contents and ambient sediments.
PubMed ID: 24967593
PMC ID: PMC4072670
Article link: PLoS One
Genes referenced: LOC105439193
Article Images: [+] show captions
|Figure 1. Rarefaction analysis of the gut content and sediment samples.Rarefaction curves of OTUs clustered for a dissimilarity of 3%. Abbreviations are as in table 1.|
|Figure 2. Shannon index of the different samples.Abbreviations are as in table 1.|
|Figure 3. Relative read abundance of different bacterial phyla above a cutoff value of 0.6%.Abbreviations are as in table 1.|
|Figure 4. The relative abundance of the 15 most abundant classes.Abbreviations are as in table 1.|
|Figure 5. Hierarchically clustered heatmap of the bacterial distribution of different communities.Double hierarchical dendrogram shows the bacterial distribution. The bacterial phylogenetic tree was calculated using the neighbor-joining method and the relationship among samples was determined by Bray-Curtis distance and the complete clustering method. The heatmap plot depicts the relative percentage of each bacterial class (variables clustering on the vertical-axis) within each sample (horizon-axis clustering). The relative values for bacterial class are indicated by color intensity with the legend indicated at the bottom of the figure.|
|Figure 6. PCA results showing the relatedness of bacterial community in the different samples.The PCA plots were constructed with the weighted UniFracPCA method. Abbreviations are as in table 1.|
References [+] :
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