Unlocking Microalgae Management in Shrimp Aquaculture

An Important Feed Source for the Aquaculture Industry

Microalgae are at the basis of all aquatic food chains, including those of the aquaculture industry. They are used as a feed product in many farming systems, including several growth stages of crustaceans, bivalve mollusks and fish species. They also provide an indirect feed source by serving as feed for zooplankton such as rotifers, Artemia and copepods, which are subsequently used as live feeds for the reared animals. But even without external dosing, they naturally occur as a part of the phytoplankton of any pond, and are an important bacterial control method (so-called “green water” farming).

Algal species with high aquaculture relevance included in the KYTOS toolbox: Chaetoceros1, Tetraselmis2, Isochrysis3, Thalassiosira4, filamentous cyanobacteria5 and other cyanobacteria5 (cells shown at different scales).

Impact of Microalgae on Farm/Hatchery Management

To properly manage algae populations and to accurately predict the risk of an outbreak of toxin-producing algae, it is essential that farmers have insights in the algae health situation in the water and gut of the animals.

Microalgae can cause positive effects during the cultivation:
  • Production of oxygen;
  • Limiting eutrophication;
  • Metabolizing nitrogenous waste products
  • Production of bioactive compounds that control the bacterial community.
Microalgae can cause negative effects during the cultivation:
  • Ideal algae growth conditions can cause rapid algae blooms and crashes;
  • Algae species composition during blooms can change rapidly over time (often seen by farmers as different pond colors);
  • Blue green algae (cyanobacteria) may produce toxins which are lethal to the shrimp.

Through these actions they control the bacterial community and this has been shown to lower disease incidence and to increase the stability of microbial system. However, some microalgae, often referred to as blue-green algae (cyanobacteria), produce toxins which can harm the cultivated organisms. In addition to toxicity problems, some species of blue-green algae can produce odorous compounds which can cause off-flavors of the cultivated organisms.

Where Can KYTOS Help?

Our standard service offering already includes exact quantification of algal abundances. We are happy to announce that over the last 6 months, our KYTOS toolbox has been further expanded with several algae-specific algorithms to empower farmers to make more informed management decisions.

Trophic index

The new KYTOS trophic index helps farmers to quantify the balance between heterotrophs (heterotrophic bacteria) and autotrophs (microalgae) in their system. This allows farmers to evaluate whether their intended management is effective (e.g. whether green water systems are dominated by autotrophs), to compare the autotroph/heterotroph balance across ponds, and to detect blooms/crashes at an early stage. See below for a commercial shrimp grow-out case on how we can use this indicator to examine our algae management performance:

  1. Two ponds on the same farm can have drastically different farming regimes (heterotroph / autotroph)
  2. These regimes are unknown to the farmer!
  3. The unstable pond experiences frequent blooms and crashes during the grow-out
  4. These blooms/crashes are often unknown to the farmer!
  5. Stable ponds go through a mixotrophic/autotrophic phase during the first 30 days
Two examples of different dynamics in trophic state of open air shrimp ponds on the same farm. Left: Unstable pond; note the frequent algae blooms and crashes throughout the cultivation. Right: Stable pond with much less abrupt changes in trophic state after the first 30 days. Legend for the index is shown on the right.
Taxonomic classification

The KYTOS toolbox has now also been updated with precise algorithms to detect and quantify the abundance of some of the most important microalgae in the aquaculture industry, including several cyanobacteria, Tetraselmis, Isochrysis, Chaetoceros and Thalassiosira. Many algal species have positive effects on the cultivation performance, while others can have disastrous effects. Therefore it is essential that farmers have insights into which algae are present in their system. For our Mediterranean enthusiasts, our algorithms will soon be expanded to include Chlorella and Nannochloropsis.

So how good are our algorithms today? See for yourself:

Microalgae population KytoFlow prediction accuracy (%)
Filamentous cyanobacteria 99.3
Other cyanobacteria 99.1
Tetraselmis 95.6
Isochrysis 97.1
Chaetoceros 96.5
Thalassiosira 98.7

Putting this into practice, we can accurately identify and forecast the blooms of these important algae groups. Some key observations from one of our commercial trials:

  1. Algae blooms and crashes of both harmful and beneficial algae happen frequently during a cultivation (~every 10 days)
  2. Did you notice the sudden loss of the important Thalassiosira diatom population? This happened during early farm management, and resulted in the complete loss of this population during the cultivation
  3. Chaetoceros appears to be the most robust diatom in the ponds
  4. Filamentous cyanobacteria make up only a small part of all the cyanobacteria, but can be the most harmful to the shrimp!
Algae identification in Shrimp grow-out pond rearing systems, both in terms of taxonomic identity and risk (beneficial/harmful).
Commercial service

Are you intrigued by our trophic index and algae identification algorithms? Looking for something else? Contact us now

1 Li Y, Boonprakob A, Gaonkar CC, Kooistra WHCF, Lange CB, Hernaândez-Becerril D, Chen Z, Moestrup Ø, Lundholm N. 2017. Diversity in the globally distributed diatom genus chaetoceros (bacillariophyceae): Three new species from warm-Temperate waters. PLoS One 12:1–38.
2 Dutertre M, Barillé L, Haure J, Cognie B. 2007. Functional responses associated with pallial organ variations in the Pacific oyster Crassostrea gigas (Thunberg, 1793). J Exp Mar Bio Ecol 352:139–151.
3 Liu Q, Pang T, Li L, Liu J, Lin W. 2014. Isochrysis sp. IOAC724S, a newly isolated, lipid-enriched, marine microalga for lipid production, and optimized cultivation conditions. Biomass and Bioenergy 60:32–40.
4 Egas C, Henríquez-Castillo C, Delherbe N, Molina E, Dos Santos AL, Lavin P, De La Iglesia R, Vaulot D, Trefault N. 2017. Short timescale dynamics of phytoplankton in Fildes Bay, Antarctica. Antarct Sci 29:217–228.
5 Ughy B, Nagy CI, Kós PB. 2015. Biomedical potential of cyanobacteria and algae. Acta Biol Szeged 59:203–224.

Tara joins the team


We are happy to welcome Tara Baele to our growing KYTOS team! Tara is an expert in targeted single-cell molecular methods and nitrogen cycle management. She holds a degree in Industrial Engineering from Ghent University.

Tara will be working on next-gen functional health metrics for both shrimp, RAS and hydroponic systems and will be running the day-to-day laboratory operations for our clients.


KytoApp: Microbiome Insights on Your Mobile Phone

Good news – we’re bringing our digital health reports directly to your mobile phone via the KytoApp.

☁️ Quick health insights via the dashboard.
📈 Detailed trending analysis of your systems.
👨‍💻 Technical support and service requests from within the App.

A teaser on the App’s base functionalities can be found in the video below. Stay tuned for future updates and use cases.

Another important step taken to make microbiome management 📈 Smarter, 🏠 Easier, and 🧪 Accessible to our partners around the world.

Android ➡️
iOS 🔜 (soon)


Tin vui – chúng tôi đưa các báo cáo vi sinh kỹ thuật số đến điện thoại di động thông qua KytoApp.

☁️ Nhận thông tin chi tiết về sức khỏe vi sinh nhanh chóng nhờ bảng điều khiển.
📈 Phân tích chi tiết xu hướng phát triển vi sinh của hệ thống nuôi.
👨‍💻 Hỗ trợ kỹ thuật và yêu cầu dịch vụ ngay trong ứng dụng.

Bạn có thể tìm thấy đoạn giới thiệu về các chức năng cơ bản của ứng dụng trong video bên dưới. Hãy theo dõi các bản cập nhật trong tương lai.

Một bước tiến quan trọng được thực hiện để quản lý hệ vi sinh vật 📈 Thông minh hơn, 🏠 Dễ dàng hơn và 🧪 Tiếp cận được với các đối tác trên khắp thế giới.

Android ➡️
iOS 🔜 (sắp có)

#microbiome #startup #aquaculture #innovation #progress

Introducing KYTOS to the Vietnamese market

Spreading the word on Microbiome Management in Vietnam!

Shrimp and Fish farmers are passing by to become informed on our technology and how it can help them make their microbiome management 📈 Smarter, 🏠 Easier, and 🧪 Accessible.

Amazing to see the wide-spread interest by farmers in Grouper, Barramundi, Squid Snail, Shrimp, hatcheries, and many others.

Are you in Vietnam and interested in a demo or more information?


Quảng bá rộng rãi công nghệ quản lý hệ vi sinh vật tại Việt Nam!

Những người nuôi tôm và cá đang ghé thăm Kytos để tìm hiểu thông tin về công nghệ mới và cách nó có thể giúp họ quản lý hệ vi sinh vật của mình 📈 Thông minh hơn, 🏠 Dễ dàng hơn và 🧪 Dễ tiếp cận.

Thật ngạc nhiên khi thấy sự quan tâm rộng rãi của nông dân nuôi cá mú, cá chẽm, ốc hương, tôm, trại giống và nhiều trại nuôi khác.

Bạn đang ở Việt Nam và quan tâm đến thử nghiệm công nghệ mới này hoặc muốn biết thêm thông tin?


Check out our KYTOS Technology stack icons!

Scientific insights form the foundation on which microbiome management must be based, but technology is the vehicle to bring these insights into the hands of those who need them.

At KYTOS we’ve been rapidly expanding our technology stack with the goal of making microbiome management 📈 Smarter, 🏠 Easier, and 🧪 Accessible.

Check out below some pieces of our software puzzle 🙂


Peter joins the team


We are happy to welcome Peter Rubbens to our growing KYTOS team! Peter is an expert on single-cell data analytics and has > 5 years of experience in the field.

With this valuable addition to the team KYTOS will be able to booster its machine learning workflows and data reporting capabilities to make microbiome management 📈 Smarter, 🏠 Easier, and 🧪 Accessible.