A ‘shrimple’ solution…

Acute hepatopancreatic necrosis disease (AHPND) is currently a huge threat to aquaculture as it causes early mortality in cultured Litopeneaus vannamei (Pacific whiteleg shrimp). The disease is caused by the ingestion of toxins generated by certain strains of the bacterium Vibrio parahaemolyticus, which is prevalent in marine environments. Cornejo-Granados et al., (2017) conducted a novel study characterizing the microbiota of wild shrimp as a reference to compare healthy and diseased cultured L. vannamei. They also analysed samples of pond sediment from hatcheries. It is one of the few studies to study the microbiota of the hepatopancreas as well as the intestine and it is the first to assess the effect of an outbreak of AHPND on the microbiota of cultured shrimp.

Seven hypervariable regions of the 16S rRNA gene were sequenced to identify species and applied a predictive metagenomic approach to infer the functionality of the shrimp metagenome. Seven regions were selected to provide reliable diversity estimates. Despite this, several of the OTUs were identified on the basis of one region and there were some discrepancies in read abundance for some of the regions and thus the diversity estimates could still be biased. However, their experimental design allows for the samples to be assessed comparatively and therefore this bias should not affect the interpretation of their results. Another limitation of this study was the small sample size (n=3) and low sequence depth. Regardless, as this study was the first to use high throughput sequencing to assess many aspects of the shrimp microbiome it provides a basis for future research to build upon using larger sampling efforts.

Cornejo-Granados et al., (2017) found the shrimp microbiota differed between organ, environment and the presence of disease. The microbiota and their predicted metagenomic functions were different between wild and cultured shrimp. Not surprisingly the cultured shrimp were significantly less diverse; this homogeneity is representative of their controlled environment. Furthermore, certain pathways were enriched depending on shrimp source. For instance, genes involved in metabolism, specifically the degradation of amino acids, were enriched in wild shrimp. These functions are integral to the immune response and remarkably were not found in cultured shrimp. The authors list in detail the specific pathways that were enriched at different functional levels however to disentangle the effects of these, perhaps more emphasis could have been placed on their impact at an organismal or ecosystem level. Independent of the shrimp source, the microbiota of the hepatopancreas and intestine was also significantly different in diversity and in immune related functions. Notably, there were significant differences in the microbiome of diseased and healthy cultured shrimp. Several bacteria and functional pathways were found to be disease specific. Interestingly, P. agglomerans was identified as a potential probiotic as it was found to be enriched in healthy and wild samples and thus the authors suggest it could be artificially enhanced in diseased shrimp. Lastly, the microbiota between the sediment and intestines of cultured shrimp was similar, suggesting a strong transfer of bacteria between the intestine and sediment.  Due to the importance of the sediment in the shrimp microbiome the authors identified bacteria that were enriched in the pond sediment of healthy shrimp that could be used for bioremediation purposes. The findings of this study are promising in their potential to control the disease.

Reviewed paper:

Cornejo-Granados, F., Lopez-Zavala, A., Gallardo-Becerra, L., Mendoza-Vargas, A., Sánchez, F., & Vichido, R. et al. (2017). Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions. Scientific Reports, 7(1). 
http://dx.doi.org/10.1038/s41598-017-11805-w