| Summary: | Microencapsulation is an advanced technique used to improve the viability of probiotics and minimize sensitivity during processing, storage, and in the gastrointestinal environment. Two dietary treatments including a control and an encapsulated probiotic, <i>Bacillus subtilis</i> E20 (EP), were used to evaluate the efficacy in improving the intestinal microbiome of white shrimp, <i>Penaeus vannamei,</i> after a 60-feeding trial. The 16S rDNA next-generation sequencing (NGS) analysis indicated that shrimp fed the EP diet generated higher amplicon reads than shrimp fed the control diet. No significant differences were observed in the α-diversity index of the intestinal microbiota of shrimp that were fed the control and EP diet. At the phylum level, <i>Proteobacteria</i> was relatively abundant in the microbiota of shrimp fed both the control and EP diet. The treatment with EP increased the expression of <i>Tenericutes, Bacteroidetes</i>, and <i>Firmicutes</i>, more than the control. The PC analysis revealed that the EP diet altered the bacterial profile in shrimp’s intestines into forming different clusters. Unique genera such as <i>Luteolibacter</i>, <i>Simkaniaceae, Haemophilus, Pirellulaceae, Filomicrobium, Sphingomonas,</i> and <i>Erysipelotrichaceae</i> UCG-003 along with well-known probiotic genera <i>Bacillus</i> and <i>Lactobacillus</i> were found in the intestine of shrimp fed the EP diet. The PCA eigenvector plots indicated a higher abundance of <i>Bacillus</i> in shrimp fed with EP diet, but a higher abundance of <i>Vibrio</i> in shrimp fed with control diet. These results suggest that encapsulated <i>B. subtilis</i> E20 can be beneficial to shrimp microbiota.
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