Microencapsulation of Bacillus subtilis E20 Probiotic, a Promising Approach for the Enrichment of Intestinal Microbiome in White Shrimp, Penaeus vannamei

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, Bacillus subtilis E20 (EP), were used to evaluate the efficacy in improving the intestinal microbiome of white shrimp, Penaeus vannamei, 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, Proteobacteria was relatively abundant in the microbiota of shrimp fed both the control and EP diet. The treatment with EP increased the expression of Tenericutes, Bacteroidetes, and Firmicutes, 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 Luteolibacter, Simkaniaceae, Haemophilus, Pirellulaceae, Filomicrobium, Sphingomonas, and Erysipelotrichaceae UCG-003 along with well-known probiotic genera Bacillus and Lactobacillus were found in the intestine of shrimp fed the EP diet. The PCA eigenvector plots indicated a higher abundance of Bacillus in shrimp fed with EP diet, but a higher abundance of Vibrio in shrimp fed with control diet. These results suggest that encapsulated B. subtilis E20 can be beneficial to shrimp microbiota.