Profile of the gut microbiota of Pacific white shrimp under industrial indoor farming system

Abstract The gut microbial communities interact with the host immunity and physiological functions. In this study, we investigated the bacterial composition in Litopenaeus vannamei shrimp’s gut and rearing water under different host (developmental stage: juvenile and adult; health status: healthy and diseased) and environmental factors (temperature 25 °C and 28 °C; and light intensity: low and high). The PCoA analysis showed that all water samples were clustered together in a quarter, whereas the gut samples spread among three quarters. In terms of functional bacteria, gut samples of adult shrimp, healthy adult shrimp, adult shrimp raised at 28 °C, and juvenile shrimp under high light intensity exhibited a higher abundance of Vibrionaceae compared to each other opposite group. Gut samples of juvenile shrimp, infected adult shrimp, juvenile shrimp with low light intensity, and adult shrimp with a water temperature of 25 °C showed a higher abundance of Pseudoaltromonadaceae bacteria compared to each other opposite group. Gut samples of juvenile shrimp, healthy adult shrimp, adult shrimp raised at a water temperature of 28 °C, and juvenile shrimp with high light intensity showed the higher abundance of Firmicutes/Bacteroidota ratio compared to each other opposite group. Our results showed that L. vannamei juveniles are more sensitive to bacterial infections; besides, water temperature of 28 °C and high light intensity groups were both important conditions improving the shrimp gut bacterial composition under industrial indoor farming systems. Key points • Bacteria diversity was higher among shrimp intestinal microbiota compared to the rearing water. • Shrimp juveniles are more sensitive to bacterial infection compared to adults. • Water temperature of 28 °C and high light intensity are recommended conditions for white shrimp aquaculture. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s00253-024-13046-0.


Fig. S1
Fig. S1 Shannon's index dilution curve of samples of L. vannamei shrimp gut or corresponding rearing water.D1 and D2 represent two farms in Dongying city; R1 and R2 represent two farms in Rizhao city; W represents Weihai city; and L represents Lianyungang city.J and A represent juvenile and adult, respectively.G and W represent the gut and water, respectively.

Fig. S2
Fig. S2 Bacterial community diversity indices in the gut and water of L. vannamei juveniles and adults at culture periods.D1 and D2 represent two farms in Dongying city; R1 and R2 represens two farms in Rizhao city; W represents Weihai city; L represents Lianyungang city; J and A represent juvenile and adult shrimp, respectively.Circles and squares represent shrimp gut and culture water, respectively.NS: not significant; *: p < 0.05; * *: p < 0.01; * * *: p < 0.001.

Fig. S3
Fig. S3 Principal coordinate analysis (PCoA) of the rearing water microbiota at each farm location based on Bray-Curtis (a) or Weighted-Unifrac (b) distances at OTU level.D1 and D2 represent two farms in Dongying city; R1 and R2 represent two farms in Rizhao city; W represents Weihai city; L represents Lianyungang city.

Fig. S4
Fig. S4 Bacterial community composition of juvenile and adult shrimp L. vannamei gut at phylum (a), family (b), or genus levels (c), respectively.The meaning of characters in label are as follows: The first character is the abbreviation of farm location, and D represents Dongying.The second character is the abbreviation of shrimp stage, and J represents juvenile while A represents adult.The third character is abbreviation of sample item, and G represents shrimp gut.

Fig. S5
Fig. S5 Comparison of core gut bacterial community of the juvenile and adult L. vannamei, raised in D1, D2, R1, and R2, at phylum, class, order and family levels, respectively.D1 and D2 represent two farms in Dongying city; R1 and R2 represent two farms in Rizhao city.

Fig. S6
Fig. S6 Total composition on gut bacterial community of juvenile and adult L. vannamei, cultured in D1, D2, R1, and R2, at family (a), or genus levels (b), respectively.The meaning of characters in label are as follows: The first character is the abbreviation of farm location, D1 and D2 represent two farms in Dongying city; R1 and R2 represent two farms in Rizhao city.The second character is the abbreviation of shrimp stage, and J represents juvenile while A represents adult.The third character is abbreviation of sample item, and G represents shrimp gut.

Fig. S7
Fig. S7 Source tracking of L. vannamei shrimp gut bacterial community estimated within a Bayesian framework in SourceTracker approach.As to the sample names, D1 and D2 represent two farms in Dongying city, R1 and R2 represent two farms in Rizhao city, J and A represent juvenile and adult shrimp, respectively, and G represents gut.

Fig. S8
Fig. S8 Structure analysis of bacterial community of L. vannamei shrimp and rearing water based on βNTI/RCbray values.As to the sample names, D1 and D2 represent two farms in Dongying city respectively, J and A represent juvenile and adult shrimp respectively, G represents gut, and W represents rearing water.

Fig. S9
Fig. S9 Canonical correlation analysis (CCA) of the gut bacterial communities and rearing water quality parameters of L. vannamei shrimp juvenile (a) and adult (b).As to the sample names, D1 and D2 represent two farms in Dongying city, R1 and R2 represent two farms in Rizhao city, J and A represent juvenile and adult shrimp respectively, G represents gut.In the figure, WT represents water temperature, DO represents dissolved oxygen, NO3-N represents nitrate, NO2-N represents nitrite, TAN represents total ammonia nitrogen, and PO4-P represents phosphate.

Fig. S10
Fig. S10 Comparison of core gut bacterial community of L. vannamei shrimp raised under different light intensities (low and high) at phylum, class, order, and family levels respectively.The first character is the abbreviation of farm location, and D represents Dongying city, R represents Rizhao city, W represents Weihai city, and L represents Lianyungang city.The second character is the abbreviation of shrimp stage, and J represents juvenile, while A represents adult.The third character is abbreviation of sample item, and G represents shrimp gut.

Table S1
Body weight and physiochemical conditions of the sampling L. vannamei at juvenile and adult stage.

Table S2
Nutrients concentration of the rearing water collected at juvenile and adult stage L. vannamei.