Optimizing shrimp production has been a challenge. A recent breakthrough sheds light on a hidden influential factor: the shrimp microbiome, the community of microbes that live in its gut.
The research, published in the scientific journal bioRxiv as a preprint by scientists from MIT, the National Center for Aquaculture and Marine Research (CENAIM), the Federal University of Santa Catarina, and the Escuela Superior Politécnica del Litoral (ESPOL), addresses the knowledge gap in the microbiome determinants of productivity, specifically animal survival and growth, for Pacific white shrimp (Penaeus vannamei).
The Role of the Microbiome in Aquaculture Success
Aquaculture, the farming of aquatic organisms, is a crucial source of protein for our growing world. However, optimizing its efficiency has been a challenge. A key factor influencing productivity is the microbiome, the complex community of microorganisms that live in and around the animals.
In this study, researchers delved into the relationship between the shrimp microbiome and production variables in the aquaculture of Pacific white shrimp (Penaeus vannamei), with the goal of understanding how manipulating this microbial community could improve shrimp production.
The Dual Role of the Microbiome: Friend or Foe?
Beneficial microbes can enhance shrimp health by aiding digestion, boosting immunity, and combating pathogens. On the other hand, harmful microbes can cause diseases and reduce growth rates. The challenge lies in achieving the right balance.
The Power of Tiny Tenants
The study analyzed samples from 610 farms across Asia and Latin America, revealing a core set of microbes consistently present in Penaeus vannamei, the most commonly farmed shrimp species. Notably, this “shrimp microbiome” included both beneficial and potentially harmful bacteria.
Researchers focused on the early stages of shrimp growth, specifically larval hatcheries, where survival rates are critical. Surprisingly, by analyzing the microbiome’s composition, they could predict approximately 50% of the variation in survival rates. This suggests a strong link between specific gut microbes and shrimp larvae health.
Genes for Growth
Interestingly, the beneficial microbes associated with higher survival rates harbored unique genes not found in wild shrimp. These genes seem to be adaptations to aquaculture environments and are involved in nutrient utilization by helping to break down proteins and produce growth factors. Essentially, these microbes act as tiny internal allies, helping shrimp larvae thrive.
Applications for Adult Shrimp Under Scrutiny
Predicting adult shrimp weight based on their microbiome proved more challenging, with only 10-20% predictability. This aligns with observations in other farm animals, suggesting that other factors play a more significant role in later growth stages. However, this does not diminish the importance of early-life microbiomes.
The Potential of Microbiome Engineering
This study highlights the potential of microbiome engineering to revolutionize shrimp aquaculture. By understanding key microbial players and their functions, researchers can develop strategies for:
- Early Intervention: The microbiome’s predictive power for larval survival emphasizes the importance of early-stage interventions to optimize shrimp health and production.
- Microbiome-based Probiotics: Designed probiotics targeting specific microbial functions, such as polysaccharide degradation, could provide a sustainable solution to improve shrimp growth and survival.
- Tailored Interventions: Understanding the complex interactions between the microbiome, environmental factors, and shrimp health is crucial to developing microbiome-based, targeted strategies.
Conclusion
Key findings from the study can be summarized as follows:
- The Microbiome as a Predictive Marker: The microbiome’s composition is a powerful predictor of shrimp larvae survival, underscoring its potential as an early indicator of host health.
- The Functional Role of the Microbiome: Beneficial microbes likely help break down complex organic materials and produce essential growth factors, contributing to shrimp growth and development.
- Complex Microbial Interactions: Tree-based models, such as Random Forest and Gradient Boosting, outperform linear models in predicting microbiome function, suggesting the complex nature of natural microbial communities.
- Environmental Factors and Adult Shrimp: Water quality parameters significantly influence average shrimp weight per pond in grow-out environments. However, individual body weight variation is only partially explained by the microbiome, highlighting the impact of other environmental factors.
- Microbiome Diversity and Engineering Potential: The study reveals untapped taxonomic and functional diversity within the shrimp microbiome, offering promising avenues for microbiome engineering. Specific gene clusters and horizontal gene transfer events suggest potential targets for developing probiotics designed to enhance shrimp production.
This research paves the way for a groundbreaking approach to shrimp aquaculture. By understanding and potentially manipulating the shrimp microbiome, we can significantly improve hatchery success—a critical step in the overall production process. Imagine fostering the growth of beneficial bacteria that enhance nutrient utilization and survival rates in juvenile shrimp!
Contact
Otto X. Cordero
Department of Civil and Environmental Engineering
MIT
Email: ottox@mit.edu
Reference (open access)
Shan, X., Li, K., Stadler, P., Borbor, M., Reyes, G., Solorzano, R., … & Cordero, O. X. (2024). Microbiome determinants of productivity in whiteleg shrimp aquaculture. bioRxiv, 2024-09.
