Unveiling the intestinal microbiome of shrimp: how age, health, and the environment influence it

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By Milthon Lujan

Graphical summary of the experiment. Source: Li et al., (2024); Appl Microbiol Biotechnol.
Graphical summary of the experiment. Source: Li et al., (2024); Appl Microbiol Biotechnol.

Shrimp aquaculture holds a prominent position in the aquaculture industry, with Pacific white shrimp (Litopenaeus vannamei) being the most cultivated species due to its high economic and nutritional value.

However, intensive shrimp farming methods often face a significant challenge: infectious diseases. These diseases, caused by various microorganisms, can lead to significant economic losses and hinder the sustainable development of the industry.

A team of scientists from the Yellow Sea Fisheries Research Institute of the Chinese Academy of Fishery Sciences, Shanghai Ocean University, and the University of Buenos Aires investigated the bacterial composition in the intestine of Litopenaeus vannamei shrimp and in the rearing water under different hosts (development stage: juvenile and adult; health status: healthy and diseased) and environmental factors (temperature 25°C and 28°C; light intensity: low and high).

The scientists aimed to understand how host factors (developmental stage, health status) and environmental factors (temperature, light intensity) interact with bacterial communities in the intestine of Pacific white shrimp (Litopenaeus vannamei). This effort adds to others that have focused on understanding the shrimp’s holobiome.

Indoor shrimp farming: a sustainable approach

Indoor industrial shrimp farming (IISF) models offer numerous advantages over traditional outdoor ponds. IISF systems such as flow-through systems (FTS) and recirculating aquaculture systems (RAS) provide controlled environments with year-round production, better water quality, and lower risk of disease outbreaks.

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However, even within controlled environments, concerns about diseases persist, particularly with increasing stocking density.

The power of the intestinal microbiome: a new frontier

Recent research points to a promising solution: the intestinal microbiome. This diverse community of microorganisms residing in the shrimp’s intestine plays a crucial role in its health, including digestion, reproduction, and overall immunity. This opens up exciting possibilities for manipulating the intestinal microbiome to enhance shrimp resilience and prevent diseases.

In the context of aquaculture, manipulating the intestinal microbiome of aquatic animals presents a promising strategy to overcome existing challenges. Beneficial microorganisms can act as “partners” within the host, providing protection against pathogens and promoting better health and growth.

Understanding the microbiome landscape in IISF

While extensive research has been conducted on the shrimp’s intestinal microbiome in traditional farming models, there is a critical knowledge gap regarding the specific bacterial communities present in IISF environments. This study, utilizing high-throughput sequencing technology, aims to close this gap by analyzing the bacterial communities in the shrimp intestine and rearing water in different IISF models. By understanding the composition and dynamics of these microbial communities, researchers can:

  • Discover potential relationships between intestinal and rearing water microbiomes in popular indoor farming models.
  • Lay the groundwork for biosecurity control strategies in IISF, ultimately promoting disease prevention and sustainable development within the industry.

Key findings

The study yielded the following findings:

  • Distinct intestinal and aquatic microbiomes: The analysis revealed a clear separation between bacterial communities in the shrimp’s intestine and the surrounding water. This suggests that the intestinal environment selectively harbors specific bacteria, potentially creating a unique ecosystem.
  • Age and health influence intestinal bacteria: Juvenile shrimp showed higher abundance of Pseudoalteromonadaceae, which may be associated with increased susceptibility to infections. Conversely, healthy adult shrimp harbored more Vibrionaceae, which could be related to greater disease resistance.
  • Environmental factors shape the intestinal microbiome: Higher water temperature (28°C) and increased light intensity favored the growth of Vibrionaceae and a higher Firmicutes/Bacteroidota ratio, both potentially beneficial for intestinal health.
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Potential benefits for the shrimp industry

These findings provide valuable insights for optimizing IISF practices:

  • Interventions targeted at juveniles: Considering their higher susceptibility to infections, additional support for intestinal health could be beneficial during the juvenile stage, potentially through probiotics or specific dietary adjustments.
  • Optimization of environmental parameters: Maintaining a water temperature of 28°C and ensuring adequate light exposure could promote the growth of beneficial bacteria in the shrimp’s intestine, which could enhance disease resistance.

By understanding how various factors shape the shrimp’s intestinal microbiome, we can develop specific strategies to:

  • Enhance disease prevention: Promote the growth of beneficial bacteria that act as natural barriers against pathogens.
  • Optimize growth and health: Foster an intestinal environment conducive to efficient nutrient absorption and overall well-being.
  • Refine IISF practices: Develop evidence-based guidelines for temperature, light, and other environmental parameters to optimize shrimp intestinal health in these systems.

Looking ahead

This study holds great promise for the future of shrimp aquaculture. By delving into the complexities of the intestinal microbiome, researchers aim to equip aquaculturists with valuable insights to improve shrimp health, reduce disease risks, and pave the way for a more sustainable and successful industry.

The study was funded by the National Key R&D Program of China, the allocated fund for the China Agriculture Research System (CARS-48), and the Central Public-Interest Scientific Institution Basal Research Fund, CAFS.

Zhi-Qiang Chang.
Key Laboratory of Sustainable Development of Marine Fisheries, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People’s Republic of China
Email: changzq@ysfri.ac.cn

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Reference (open access)
Li, M., Ghonimy, A., Chen, DQ. et al. Profile of the gut microbiota of Pacific white shrimp under industrial indoor farming system. Appl Microbiol Biotechnol 108, 225 (2024). https://doi.org/10.1007/s00253-024-13046-0