Yamazaki Y et al. (2016), Individual Apostichopus japonicus fecal microbi...

ECB-ART-44527

Sci Rep 2016 Feb 24;6:21631. doi: 10.1038/srep21631.

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Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps.

Yamazaki Y , Meirelles PM , Mino S , Suda W , Oshima K , Hattori M , Thompson FL , Sakai Y , Sawabe T , Sawabe T .

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Gut microbiome shapes various aspects of a host''s physiology, but these functions in aquatic animal hosts have yet to be fully investigated. The sea cucumber Apostichopus japonicus Selenka is one such example. The large growth gap in their body size has delayed the development of intensive aquaculture, nevertheless the species is in urgent need of conservation. To understand possible contributions of the gut microbiome to its host''s growth, individual fecal microbiome comparisons were performed. High-throughput 16S rRNA sequencing revealed significantly different microbiota in larger and smaller individuals; Rhodobacterales in particular was the most significantly abundant bacterial group in the larger specimens. Further shotgun metagenome of representative samples revealed a significant abundance of microbiome retaining polyhydroxybutyrate (PHB) metabolism genes in the largest individual. The PHB metabolism reads were potentially derived from Rhodobacterales. These results imply a possible link between microbial PHB producers and potential growth promotion in Deuterostomia marine invertebrates.

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Species referenced: Echinodermata
Genes referenced: LOC100887844 LOC115925415 pcsk2 phb

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	Figure 1. Growth gaps observed in the cultured sea cucumbers.(a) Representatives of the larger and the smaller sea cucumbers cultured under identical conditions are displayed from lower to upper. (b) A histogram for body weight of sea cucumbers showed right-skewed size distribution. These specimens are 20 months old, and were raised on artificial diets for 17 months. For the final two months in the Kumaishi farm, the animals were fed with naturally occurred diatoms before being studied. Size distributions of the larger and smaller individuals used in this study were highlighted in green and purple, respectively. (c) Box plot for actual body weights from 10 larger and 10 smaller individuals used in this study. The body weight averages of two groups, “larger” and “smaller”, were statistically significant.
	Figure 2. The microbiota of larger and smaller sea cucumbers feces are different.(a) The larger and the smaller sea cucumbers clustered individually, and seawater sample differed from sea cucumber samples. (b) Ranking of the order level abundances in fecal microbiota of the larger (green) and the smaller (purple) individuals. Only significant taxa were shown in this bar plot; Rhodobacterales, Desulfobacterales and Oceanospirillales were significantly more abundant in the larger individuals, Marinicellales, Acidimicrobiales were more abundant in the smaller individuals.
	Figure 3. Microbial diversity comparisons between larger and smaller Apostichopus japonicus individuals.(a) Species richness, (b) Shannon index, (c) evenness, and (d) unweighted UniFrac-based 2D PCoA plot was based on all OTUs from the larger, the smaller sea cucumbers and seawater sample. Percent variation expected were PC1 15.69%, PC2 10.99%. Samples indicated with arrows were used for functional metagenomic analysis. The larger sea cucumbers, the smaller ones, and seawater sample are indicated in green, purple, and blue, respectively.
	Figure 4. An extended error bar plot showing more abundant features in the largest sea cucumber.Green bars indicate the largest sea cucumber and purple indicate the smallest sea cucumber. Proportion (left side) means a possible abundance of microbes possessing each functional feature, and difference between proportions (=effect sizes) for each feature is indicated by a green dot. For this analysis, features were filtered by q value (0.05) and effect size (0.05). Relative abundances of metagenome reads related to polyhydroxybutyrate (PHB) metabolism and butyrate metabolism were more abundant in the largest individual.

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