Enterococcus faecium are associated with the modification of gut microbiota and shrimp post-larvae survival

BACKGROUND: Probiotics are widely used to promote host health. Compared to mammals and terrestrial invertebrates, little is known the role of probiotics in aquatic invertebrates. In this study, eighteen tanks with eight hundred of shrimp post-larvae individuals each were randomly grouped into three groups, one is shrimps administered with E. faecium as probiotic (Tre) and others are shrimps without probiotic-treatment (CK1: blank control, CK2: medium control). We investigated the correlations between a kind of commercial Enterococcus faecium (E. faecium) powder and microbiota composition with function potentials in shrimp post-larvae gut. RESULTS: We sequenced the 16S rRNA gene (V4) of gut samples to assess diversity and composition of the shrimp gut microbiome and used differential abundance and Tax4Fun2 analyses to identify the differences of taxonomy and predicted function between different treatment groups. The ingested probiotic bacteria (E. faecium) were tracked in gut microbiota of Tre and the shrimps here showed the best growth performance especially in survival ratio (SR). The distribution of SR across samples was similar to that in PCoA plot based on Bray-Curits and two subgroups generated (SL: SR < 70%, SH: SR ≥ 70%). The gut microbiota structure and predicted function were correlated with both treatment and SR, and SR was a far more important factor driving taxonomic and functional differences than treatment. Both Tre and SH showed a low and uneven community species and shorted phylogenetic distance. We detected a shift in composition profile at phylum and genus level and further identified ten OTUs as relevant taxa that both closely associated with treatment and SR. The partial least squares path model further supported the important role of relevant taxa related to shrimp survival ratio. CONCLUSIONS: Overall, we found gut microbiota correlated to both shrimp survival and ingested probiotic bacteria (E. faecium). These correlations should not be dismissed without merit and will uncover a promising strategy for developing novel probiotics through certain consortium of gut microbiota. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-021-00152-x.