Intestinal Microbiota of White Shrimp Penaeus vannamei Under Intensive Cultivation Conditions in Ecuador

Abstract

The goal of the study was to characterize the intestinal tract bacterial microbiota composition of Penaeus vannamei in intensive commercial ponds in Ecuador, comparing two shrimp-farming phases: nursery and harvest. Bacterial microbiota was examined by sequencing amplicons V2-V3 of the 16S rRNA using Ion Torrent technology. Archaea sequences were detected in both phases. Sequence analyses revealed quantitative and qualitative differences between the nursery phase and the harvest phase in shrimp intestinal microbiota composition. The main differences were observed at the phylum level during the nursery phase, and the prevailing phyla were CKC4 (37.3%), Proteobacteria (29.8%), Actinobacteria (11.6%), and Firmicutes (10.1%). In the harvest phase, the prevailing phyla were Proteobacteria (28.4%), Chloroflexi (19.9%), and Actinobacteria (15.1%). At the genus level, microbiota from the nursery phase showed greater relative abundances of CKC4 uncultured bacterium (37%) and Escherichia-Shigella (18%). On the contrary, in the microbiota of harvested shrimp, the prevailing genera were uncultured Caldilinea (19%) and Alphaproteobacteria with no other assigned rate (10%). The analysis of similarity ANOSIM test (beta diversity) indicated significant differences between the shrimp microbiota for these two farming phases. Similarly, alfa-diversity analysis (Chao1) indicated that the microbiota at harvest was far more diverse than the microbiota during the nursery phase, which showed a homogeneous composition. These results suggest that shrimp microbiota diversify their composition during intensive farming. The present work offers the most detailed description of the microbiota of P. vannamei under commercial production conditions to date.

A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota

“…We found an enrichment of Caldilinea in all marine shrimps under farm conditions, which is in agreement with the high abundance previously observed of this genus for L. vannamei under intensive cultured conditions ( Gainza et al, 2017 ). The denitrification activity characterizes this bacterium, and interestingly it has been found with high abundance in landfills under chemical-stressed conditions ( Wu et al, 2017 ).…”

Effect of mannan oligosaccharides on the microbiota and productivity parameters of Litopenaeus vannamei shrimp under intensive cultivation in Ecuador

“…The promotion of changes in the composition of the intestinal microbiota is a key component of the case for using MOS as prebiotics, but this aspect has also been one of the least developed. The composition of the microbiota of shrimp under control conditions is consistent with previous research on this species, agreeing that Proteobacteria is the dominant phylum, with relative abundance levels between 28 and 70% [44][45][46][47][48][53][54][55][56][57] . Other phyla showing high abundance under control conditions were Bacteroidetes (22%) and Actinobacteria (11%), whose values matched those in some of the previous studies; however, overall, those studies showed variable relative abundance levels.…”

“…For cultivated crustaceans such as L. vannamei, information on the functionality and structuring of microbiota is very limited. Latterly, advances in NGS have allowed develop research on crustaceans microbiota, as recently addressed in some studies [44][45][46][47][48] . These investigations have been based on modulating the L. vannamei microbiota through nutritional challenges in laboratory conditions.…”

Biofilm consumption shapes the intestinal microbiota of shrimp (Penaeus vannamei )

“…In fish for example, the absence of gastrointestinal microbiota has severe developmental consequences such as late development of epithelial cells, abnormal enterocytes, lower efficiency in the assimilation of proteins and other macromolecules, adverse effect on cholesterol metabolism, depressed immune system, abnormal development of lymphoid tissues associated with the intestine, lower growth and higher mortality (Nayak, ). The understanding of the microbiota of the most important shrimp regarding crustacean aquaculture ( Penaeus vannamei ) remains insufficient compared to vertebrates, including terrestrial livestock and finfish species (Gainza, Ramírez, Ramos, & Romero, ).…”