RELATIONSHIP BETWEEN ALPHA DIVERSITY AND Rhodobacteraceae/Vibrionales RATIO AS AN INDICATOR OF GUT HEALTH OF WHITELEG SHRIMP LITOPENAEUS VANNAMEI

The use of the 16S rRNA marker genes is gaining momentum as a practical tool to appraise the role of intestinal microbiota in shrimp culture. High-throughput sequencing produces an enormous amount of data and results are often expressed by the relative abundance of bacteria taxa, however this approach introduces a bias in the absence of microbial load quantification. Latest advance in managing 16S sequencing data contemplates the log ratio between bacteria, which automatically cancels this bias, by comparing the ratios of different taxa between samples instead of the relative abundance of individual taxa (Morton et al., 2019). We applied this approach to shrimp microbiota data sets by looking at the relationship between alpha diversity and the ratio between two important taxa in the shrimp intestinal microbiota: the family Rhodobacteraceae and the class Vibrionales. Indeed Rhodobacteraceae includes many beneficial bacteria species while Vibrionales contains well-known opportunist and pathogenic species suggesting the Rhodobacteriaceae/Vibrionales (R/V) ratio as a potential biomarker of gut microbial health and welfare in shrimp.

Data were compiled from 4 independent pond trials performed in Vietnam over the grows-out phase, hence covering a variety of dietary, environmental and sanitary conditions. A total of 100 guts and 63 digestive glands (DG) were included with the same molecular approach applied for DNA extraction, PCR primers and bioinformatics processing.

High-throughput sequencing of the 16S rRNA V3-V4 region was analysed with DADA2 independently per trial, then Shannon diversity index and ratio Rhodobacteraceae/Vibrionales values were computed to test a potential correlation on QIIME2 (Bolyen et al., 2019), a python-based microbiome platform.

Results showed a highly significant correlation between the R/V log ratio and Shannon alpha diversity index (r = 0.544; P = 0.000; Fig. 1). Interestingly, gut samples had a higher ratio than the digestive glands, and non-challenged shrimps also harboured a higher ratio than challenged ones (P < 0.05).

The study identifies the R/V log ratio as a potential biomarker of intestinal microbial diversity typically associated with intestinal and shrimp health and robustness. Future studies should validate this simple and more readily accessible ratio as a potential biomarker and predictor of grow-out crop performance.