Next Generation Sequencing Technology: Discover the Microbial Diversity in Your Shrimp Pond

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Next Generation Sequencing Technology: Discover the Microbial Diversity in Your Shrimp Pond

December 11, 2024 by Revfvi Al Ghaney Rizal

Shrimp diseases are a recurring issue in the world of shrimp farming. This persistent challenge continues to haunt farmers, especially when farm management practices are not implemented properly.

One of the most pressing issues for shrimp farmers is managing water quality. A notable example is Acute Hepatopancreatic Necrosis Disease (AHPND), also commonly known as Early Mortality Syndrome (EMS). AHPND/EMS is often triggered by poor water conditions, high organic waste levels, and the proliferation of harmful microbes like Vibrio species, the primary pathogen responsible for this disease.

The Importance of Water Quality in Maintaining Microbial Ecosystem Balance

The water quality in shrimp farms is heavily influenced by the number and types of microbes present. Microbes play a crucial role in maintaining ecosystem balance, which is essential for sustainable shrimp farming.

However, when this balance is disrupted, the water can become a breeding ground for pathogenic agents. A higher dominance of pathogenic bacteria such as Vibrio over beneficial probiotic bacteria can trigger harmful diseases in vannamei shrimp, resulting in significant losses.

This highlights the critical importance of water quality management for successful shrimp farming. Regular pond monitoring is necessary, especially to assess biological parameters and microbial diversity. However, identifying microbial diversity in shrimp farms can often be a challenging task.

Understanding Microbial Diversity with Next Generation Sequencing (NGS)

One of the most advanced methods to assess microbial diversity is Next Generation Sequencing (NGS). NGS provides an in-depth analysis of various bacteria, viruses, and fungi present in water samples. This technology allows for accurate microbial identification at the species level, offering several advantages:

1. High sensitivity

2. Fast turnaround time

3. Comprehensive data

Compared to traditional methods, NGS reveals the true microbial diversity, offering a more precise base-level identification than conventional culture-based techniques. With NGS, farmers can obtain a detailed microbial profile, highlighting the dominant microbial populations in their ponds.

NGS vs. Traditional Bacterial Culture Methods

When compared to traditional bacterial culture methods, NGS stands out for its accuracy and speed. Conventional culture methods require a longer processing time and can only identify microbes that can survive and grow in laboratory conditions. As a result, these methods often fail to provide a complete picture of microbial diversity.

In contrast, NGS can rapidly and accurately assess water conditions and microbial diversity without the need for labor-intensive culturing. This allows shrimp farmers to make quick, informed decisions to manage their ponds effectively. NGS can directly detect a wide range of pathogens, including bacteria, viruses, and fungi, eliminating the need for time-consuming culture processes.

Nusantics: The First NGS Service Provider for Shrimp Farms in Indonesia

Check your pond now with Nusantics!
Nusantics offers the first and only NGS service in Indonesia tailored for shrimp farming needs. With the AquaCheck service, you can analyze microbial diversity in water samples, both before and after fermentation, ensuring the quality of your water sources and pond water.

Additionally, ProCheck helps you assess microbial diversity in feed mixtures or probiotic products, supporting effective quality control processes.

Boost your farm's productivity with a more scientific and reliable approach!

Contact CeKolam’s admin now for more information and orders: 0882-1877-4777.

References

10 Jenis Penyakit Udang Vaname Kronis & Tips Mengatasinya
Chen L., Liu P., Evans T.C., Ettwiller L.M. (2017). DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification. Science, 355, 752–756.
Sabat A.J., Van Zanten E., Akkerboom V., Wisselink G., Van Slochteren K., de Boer R.F., Friedrich A.W., Rossen J.W.A. (2017). Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification: Increased discrimination of closely related species. Scientific Reports, 7, DOI: 10.1038/s41598-017-03458-6.

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