Bacterial biota of shrimp intestine is significantly modified by the use of a probiotic mixture: a high throughput sequencing approach

Abstract

The use of probiotics is a common practice of current shrimp aquaculture. Despite the immunophysiological responses that have been measured in shrimp exposed to probiotics, no information is currently available on the effect of this practice on the intestinal microbiota. The objective of this work was to evaluate the effect of a probiotic mixture on the intestinal microbiota of shrimp cultured under farm conditions. A culture-independent method based on high-throughput-sequencing (16S rRNA) was used to examine intestinal bacterial communities. A traditional system (without probiotics) was used as the reference. Targeted metagenomics analysis revealed that the probiotic mixture was based on bacteria in the phyla Proteobacteria and Firmicutes. A total of 23 species of bacteria were detected in the probiotic mixture; of these, 11 were detected in the intestine of shrimp reared in both systems, and 12 were novel for the system. Eight of the novel species were detected in shrimp cultured with the probiotic mixture; however, none of these novel species were related to marine or inclusively aquacultural environments, and only one (Bacillus subtilis) was recognized as probiotic for shrimp. The use of the probiotic mixture modified the bacterial profile of the shrimp intestine; however, most of the bacteria incorporated into the intestine were nonindigenous to the marine environment with no previous evidence of probiotic effects on any marine organism. The use of this probiotic mixture may represent a risk of causing environmental imbalances, particularly because farms using these types of probiotic mixtures discharge their effluents directly into the ocean without prior treatment.

The effects of dietary probiotic Bacilli (Bacillus subtilisandBacillus licheniformis) on growth performance, feed efficiency, body composition and immune parameters of whiteleg shrimp (Litopenaeus vannamei) postlarvae

“…turn, improve digestive enzymes activity, growth performance and immune status of shrimp(Kongnum & Hongpattarakere, 2012;Laranja et al, 2017;Li et al, 2007;Lin et al, 2008;Vargas-Albores et al, 2017;Zokaeifar et al, 2012). In the present study, the results showed that dietary commetcial probiotic Bacilli (B. subtilis and B. licheniformis) significantly improved the growth performance and feed utilization(Table 2).…”

“…Over the past decades, there was increasing interest towards administration of dietary probiotic in crustacean such as penaeid shrimp (Chai, Song, Chen, Xu & Huang, ; Farzanfar, ; Hoseinifar, Zare & Merrifield, ; Moriarty, ; Niu et al., ). It is now well‐documented that probiotics modulate gut microbiota, which, in turn, improve digestive enzymes activity, growth performance and immune status of shrimp (Kongnum & Hongpattarakere, ; Laranja et al., ; Li et al., ; Lin et al., ; Vargas‐Albores et al., ; Zokaeifar et al., ). In the present study, the results showed that dietary commetcial probiotic Bacilli ( B. subtilis and B. licheniformis ) significantly improved the growth performance and feed utilization (Table ).…”

The Use of Bioinformatic Tools in Symbiosis and Co-Evolution Studies

“…The main difference between each site is the proportion of each taxa, which reflects the conditions of each environment [6,[8][9][10][39][40][41]. A similar behavior has been observed when studying the microbiome in different animal models where the phyla: Proteobacteria, Acitnobacteria, Firmicutes, and Bacteroidetes have been reported among those of greater relative abundance [4,9,39,[42][43][44][45][46]. This shows that microbial communities are highly dynamic where the physical-chemical factors of the site, health status, and nutrition shape the metagenome and can determine how reactive a microbial community is to environmental changes.…”

“…The use of genomic tools has made possible to identify the core microbiome of different organisms, given that, despite living in different habitats, they share similar bacterial communities, which implies the existence of biological filters that shape the bacterium-host interactions, resulting in a stable relationship with the holobiont [2,28,[45][46][47]. In the case of Apis mellifera, a global core microbiome formed by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria has been identified, together with a high amount of lactic acid bacteria which have a beneficial activity in the health of the host organism due to their involvement in the immunomodulation of the intestinal microflora [25,39,48].…”

“…This could be due to the fact that alterations in the microbiome composition skew the association between the host and the microbiome producing dysbiosis and increasing the number of opportunistic pathogens [6,12,13,16,27,39,45,52]. In marine environments, the continual presence of pathogens has been observed in environmental samples [16,44] and in several marine organisms (L. vannamei and M. nipponense) [17,18,39,45,46]. The continual presence of pathogens in low proportion has been reported during the life cycle of these species, suggesting an active in situ infection in which the host has co-evolved with the parasitic organisms and developed mechanisms that cope with the pathogenic mechanisms of the parasites [13, 16,17,27,45,46,52].…”