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.

New aquaculture alliance with Aqua Pharma Group & eFishery

Aquaculture disease management and dynamic dosing expert Aqua Pharma are joining forces with microbial fingerprinting experts KYTOS to develop SEATRU™ – a unique new service platform offering shrimp farmers worldwide effective microbial control through precise dosing recommendations.
The initiative is set to start later this month (June 2022) with a two-year research project based in Indonesia with local partner eFishery, the world’s largest aquaculture tech start-up.

Our priority at Aqua Pharma is to provide disease prevention and control systems to the aquaculture industry with fish and shrimp welfare at the forefront. We are delighted to have teamed up with KYTOS to further develop SEATRU™ – a tool which will use the power of KYTOS technology to read the aquaculture microbiome of farms, anticipating and reducing disease thanks to individually tailored and precise dosing of eco-friendly health management solutions.

Markus Wu, Head of Office Indonesia for Solvay and Aqua Pharma at Aqua Pharma Group

Shrimp farmers are currently hampered by a lack of reliable data on water quality and animal health, resulting in frequent unpredictable disease outbreaks. SEATRU™ will allow farmers to adopt a preventative management approach, using best-in-class products like Aqualisan® to increase production, sustainability and profitability.

Markus Wu (Aqua Pharma) Priyandaru Agung (eFishery), Marc Indigne (COO, Kytos)

KYTOS specializes in analysing data of individual microbial cells and leverages that big data to create a holistic view of the health situation of aquaculture systems. Our expertise in microbial fingerprinting technology is a perfect fit with our joint vision of unlocking sustainable aquaculture through precision farming. Together our work on the SEATRU™ concept is transforming aquaculture by researching and developing advanced technologies in microbial monitoring, animal gut health, disinfectant treatments and artificial intelligence to create stable water conditions and ensure increased performance.

Ruben Props, co-founder and CEO at KYTOS

According to WWF*, over 55% of the shrimp consumed worldwide is farmed, with a market growth of 8% over the past decade. The annual loss to the shrimp industry as a result of disease is estimated at $6 billion per year. The research project is due to run from June 2022 until mid-2024, after which commercial scaling will follow.

Our main objective is to provide shrimp farmers in Indonesia with peace of mind and the tools to produce a stable performance and improved harvests throughout the year. The SEATRU™ concept brings that stability and potential for growth to farmers. Disease prevention is the number one challenge facing shrimp aquaculture today. With disease able to completely wipe out a pond in five days the sector urgently needs effective preventative methods. Innovative new pond reading technologies combined with eco-friendly products like Aqualisan® for shrimp pond management have huge potential to improve the welfare of the shrimp and the profitability of the sector.

Gibran Huzaifah, CEO of eFishery


Backed by parent companies Solvay, the 10B EUR global leader in sustainable materials and solutions, and Aquatiq, a Norwegian leader in food safety, Aqua Pharma Group develops and delivers disease prevention and control systems for the aquaculture industry. Its concepts and innovations ensure minimal environmental impact and maximum animal welfare and contribute to the successful scaling of sustainably managed fish and shrimp to meet the global growing demand for healthy proteins


KYTOS is a microbiome technology company developing microbiome management solutions at the frontier of technological innovation. Originating at the Center for Microbial Ecology and Technology (CMET) at Ghent University, it builds on decades of world-leading expertise in the management of microbial communities. KYTOS transforms its partners into expert microbiome health stewards by empowering them with a unique blend of data science, technology, and microbial ecology insights.

ABOUT eFishery

eFishery believes that aquaculture is the future. Using technological advancements it is constructing an end-to-end value chain for fish and shrimp farming businesses, resulting in an integrated, sustainable ecosystem resilient enough to strengthen global food security for the future. eFishery aims to ensure aquaculture provides the world with its main source of animal protein, one not only rich in nutrients but accessible to everyone.

Sea bass

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Shrimp Microbiome Health Tools

Detailed overview of the microbial health in your system

Microbial load
High bacterial loads increase the risk for disease and phytoplankton blooms.

Microbial load
High bacterial loads increase the risk for disease and phytoplankton blooms.

Microbial load
High bacterial loads increase the risk for disease and phytoplankton blooms.

Microbial load
High bacterial loads increase the risk for disease and phytoplankton blooms.

Shrimp Microbiome Health Tools

Detailed overview of the microbial health in your system

Microbial load
High bacterial loads increase the risk for disease and phytoplankton blooms.

Microbial load
High bacterial loads increase the risk for disease and phytoplankton blooms.

Microbial load
High bacterial loads increase the risk for disease and phytoplankton blooms.

Microbial load
High bacterial loads increase the risk for disease and phytoplankton blooms.

Microbiome Health Assessment In Greenhouses – Part 1

The Great Unknown: Microbes in Greenhouses

With crop losses of billions of dollars annually, microbial diseases pose a large threat for the hydroponics sector. As most farmers know, the recirculation water in a hydroponics installation is one of the main sources responsible for the introduction and spread (so-called “vector”) of phytopathogens. Hydroponics systems therefore require almost constant water management to control microbial disease pressures on the crops. To be able to manage these systems KYTOS helps farmers and other stakeholders:

  • Identify the water sources where there is a low microbial health situations
  • Connect the health deviations with climate and other operational factors
  • Assess the risk for a disease outbreak
  • Take action via the right treatments

Unfortunately, information regarding the microbiome health within hydroponics greenhouses is incredibly scarce. This makes it difficult for farmers, but also solution providers to know what’s really happening in their greenhouse(s). KYTOS partnered with Tomato Masters to finally shed a first light on the microbial health status within tomato greenhouses. We are proud to share our results with the world.

Our Sampling Approach for Three Greenhouses

Each greenhouse is unique and we thus had to optimize our sampling scheme for each one of them. The first two sampled greenhouses consisted of four tap sections (“kraanvakken“) with individual irrigation systems. The samples were taken from the main tap of the greenhouse (“hoofdkraan“) and from the distribution line at each of the four tap sections (“druppelleiding“). The third greenhouse had a different tap section layout and there we sampled the 204 individual drains (“goten“) that are used to collect drainwater from the plant substrate.

Sampling with our KytoVials is so easy and quick, the team was able to collect over 220 biosecure samples in < 1 hour!

Schematic illustration of the layout of the sampled greenhouses at Tomato Masters. A) Layout of the greenhouses at which the main tap and distribution line in each of the tap sections was sampled. B) Layout of the greenhouse where individual drains were sampled.


Tap Sections House Different Microbiomes

Our supervised learning toolbox KytoFlow was able to pick up some important observations (Figure 1). The average bacterial load in the main tap and irrigation water of the tap sections were almost identical with only a maximum difference of 3x between the tap sections.

Our recently developed algorithm for the detection of common water molds such as oomycetes spores (e.g. Pythium, Phytophthora) revealed that the lowest load was observed at the main tap while larger differences in oomycete load were found across the tap sections (up to 100x).

In simple terms: the microbial water quality strongly deteriorated over the tap sections specifically due to the accumulation of water mold spores. Tap sections 3 and 4 were found to be of higher risk for greenhouse #1, and sections 2 and 3 for greenhouse #2.

Fun fact: A big advantage of our Oomycetes algorithm is that it is able to identify the zoospores, which are the motile phenotypes of these water molds, and pose the highest risk for disease migration.

Figure 1. Bacterial load and oomycetes risk indicators measured in the main tap and individual tap sections of the two first greenhouses.

Drain Microbiomes Differ Across Tap Sections

Greenhouses are known to have hotspots for microbe-related problems as well as differences in crop performances between production rows. The drains in a greenhouse carry the microbiome from the input water to the plant and substrate microbiomes. The microbiome can thus change considerably due to differences in plant exudates, climate, or farm management. For Tomato Masters, we completely screened the microbial water quality of all production rows (Figure 2).

Bacterial and Water Mold Pressures Can Differ Strongly Between Drains

  • 10 % of all drains could be classified as hotspots (based on IQR of 1.5).
  • Every tap section has hotspots for water molds and bacterial growth.
  • Tap sections #1 (orange) and #2 (red) were the cleanest for water molds, but there were many drains with over 1000-fold higher spore loads.
  • Tap sections #2 (blue) and #4 (teal) had elevated spore loads for nearly all drains.

Diversity and Microbiome Types are Dependent on Tap Section

  • The microbial diversity, which is a proxy for a healthy and resilient microbiome, showed a wavy pattern throughout the greenhouse.
  • Drains with the highest diversity were located at the beginning and end of the tap sections.
  • We identified four different types of microbiome in the drains. Tap sections 3 and 4 were strongly enriched in other microbiome types than the clean drains (1 and 2). More than 50 % of all drains had a type 3 or type 4 microbiome.
Figure 2. Bacterial load, oomycetes risk indicator, diversity and microbiome types measured in 204 individual, consecutive gutters of a greenhouse. Each label color corresponds to a tap section in the greenhouse. The black lines are smoothed lowess fits and highlight the trends in the data.

Take Home

  • Microbial hotspots exist in greenhouses and they can be found both within individual tap sections, as well as concentrated within specific tap sections.
  • There are gradual gradients in microbiome characteristics found across the drains, suggesting climate and design related impacts (ongoing work – part 2).
  • Both incoming and irrigation water can be highly variable in quality despite originating from the same input water.
  • Different drains house different microbiome types, bacterial load and diversity and oomycetes load. Targeted and precise management of these hotpots will be the key.

We hope these data have showcased that the routine analysis of microbiomes is crucial and and that it is the key to improved microbiome management. We believe that farmers can now use these data feeds to create more stable microbial water quality conditions for the benefit of their crops via the targeted use of biostimulants, disinfectants, and other products.

Stay tuned for the launch of our horticulture services which will include the following benefits:

  • Weekly analysis and next business day reporting
  • Logistics arranged for you
  • Flexible sampling schemes
  • Fixed monthly cost

So What’s Next?

In part 2 of this work we’ll discuss more in-depth technical results on how we can relate these microbiome health characteristics to farm KPIs such as row-based production numbers and climate measurements.

About Tomato Masters

Tomato Masters is an innovative Flemish family business that is specialized in the hydroponic farming of tomatoes. The company owns 21 hectares of horticulture, spread across over four greenhouses. Sustainability is one of the key company values and therefore there is a strong effort to use water as efficiently as possible.

Curious about the microbiome health status of your greenhouses?

KYTOS – I&V Bio collaboration makes microbiome management accessible

A Need for Rapid Logistics and Local Microbiome Analysis

Aquaculture has an enormous potential to ensure food security in a sustainable way. Animal health and water quality are therefore crucial aspects. Frequent and unpredictable disease outbreaks are detrimental to farm yields. By better controlling the microbiome based on robust and detailed data, the industry can take the necessary next step towards sustainable and reproducible farming.

KYTOS and I&V Bio are now joining forces to bring rapid sample logistics (I&V Bio) and local microbiome analysis (KYTOS) to the six most important shrimp producing countries (Thailand, Indonesia, India, Vietnam, Ecuador and Bangladesh). The partnership will install local and independent KYTOS labs to serve aquaculture farms and hatcheries with cutting-edge high throughput microbiome management tools.

The partnership combines I&V Bio’s long-standing expertise in serving aquaculture clients every single day of the year with KYTOS’s novel microbial fingerprinting technology that brings a holistic view on the aquaculture microbiome health. Vietnam has been selected as the first country where a central sample collection point, equipped with KYTOS’s automated microbiome analysis platform will be established. The other countries will follow swiftly. 

Today, KYTOS technology can already characterize most of the microbial life (fungi, bacteria and algae) in the water, sediment and shrimp of a pond. Functional indicators, devised using machine learning, connect these data to farm actions such as biofloc formation, water maturation, and microalgae blooms. This ever-expanding list of indicators will help aquaculture farmers to shift the focus from mitigating diseases to an altogether improved management of the microbiome in their systems.

Enabling Precision Farming in Aquaculture

In the fields of water and animal treatments, KYTOS can now open the microbial black box in aquaculture systems by using so-called “microbial fingerprints”. This assessment provides farmers with microbial health insights that empowers them to take targeted actions to optimize animal health and production yields.

“The need for improved health management and disease prevention is as critical today as ever. Effective biosecurity will always be key to boost the commercial viability and environmental responsibility of the shrimp farming industry.“

Frank Indigne, CEO of I&V Bio

KYTOS uses big data and artificial intelligence to reduce aquaculture’s unpredictability by creating practical tools that help all stakeholders make informed management decisions to improve their farm performance. 

Shrimp aquaculture has largely been deprived of the benefits of new microbiome technologies and knowledge. At KYTOS, we’re on a mission to change that status quo. This partnership is an important step to bring our microbial fingerprinting platform to the farmers across the world. By working closely with all stakeholders in the industry we will create a unique opportunity to manage the microbiome together, for the benefit of the industry.

Ruben Props, CEO of KYTOS

About I&V Bio

I&V Bio specializes in the daily and fresh delivery of its live feeds and solutions to the aquaculture industry. 8 years ago, the founders Frank Indigne and Luk Van Nieuwenhove started working on a revolutionary solution that has taken the Artemia-hatching burden away from shrimp hatcheries by creating Artemia hatching facilities. These facilities combine know-how, experience and new technologies to produce Artemia nauplii in a professional and industrial way. Currently, the I&V Bio Group has established Nauplii Centers in 6 countries: Thailand, India (3), Indonesia, Vietnam,  Ecuador and  Bangladesh. 

All the I&V Bio Artemia Centers use a patented technology that allows them to offer pure undamaged Artemia nauplii (Instar1) free of the shell and other impurities, and free of Vibrio. The Artemia nauplii are disinfected, brought into suspended animation and de-watered until a consistent unique live-paste is achieved. The Artemia nauplii are ready to use and can be scooped from the tray directly into the shrimp tank. I&V Bio’s key to success is our guarantee to supply our customers with daily fresh, clean and  disinfected vibrio-free products.


KYTOS is a microbiome technology company developing microbiome management solutions at the frontier of technological innovation. We have our origins in the Center for Microbial Ecology and Technology (CMET) at Ghent University, from which we build on decades of world-leading expertise in the management of microbial communities. We transform our partners into expert microbiome health stewards by empowering them with a unique blend of data science, technology, and microbial ecology insights.  

KYTOS toolbox Expanded with Oomycetes Detection Algorithm

Chicory: a Unique Crop Cultivation

Chicory (“witloof“) is a traditional Belgian vegetable, which, unlike most other vegetables, has to be grown twice. The chicory is sown in regular soil to allow the development of roots. The roots are then harvested from the field and planted in trays, stacked vertically in large, dark storehouses. Recirculating water circuits across the trays distribute nutrient solutions to the crops, making them highly susceptible to diseases.

Oomycetes Plague the Horticulture Industry

Oomycetes are a group of fungus-like microorganisms that include a wide range of pathogens. They are among the most problematic groups of disease-causing organisms in both agri- and aquaculture. Some of the most damaging diseases include potato late blight (“aardappelziekte“), downy mildew (“valse meeldauw“), and root rot (“wortelrot“).

Chicory or “Witloof” cultivation is traditionally farmed in vertically stacked hydroponic systems.

New KYTOS offering Helps to Take Immediate Action Against Oomycetes

With crop losses of billions of dollars annually, these diseases pose a large threat for global food security. The genera Pythium and Phytophthora affect a wide range of crops and are difficult to treat and get rid of. During their life cycle, oomycetes produce spores which can spread the disease quickly. This spread is amplified in hydroponic installations though intensive water recirculation.

We are happy to announce:

  • A novel Oomycetes detection algorithm has been added to our growing KYTOS toolbox.
  • KYTOS services can now empower horticulture companies even more to take targeted and timely management strategy for their water system.
  • Routine microbiome health surveillance is key to assessing root rot risks for each batch.

KYTOS Partners up with Innovators

Primalof, an innovative Flemish company, is specialized in the hydroponic cultivation of chicory. Primalof is working with Praktijkpunt Landbouw Vlaams-Brabant to optimize their water reuse, in order to further improve on the environmental friendliness of their production processes. To help assess their water treatment and guarantee microbial water quality, our microbiome health service was used, which included our latest KYTOS algorithm for the detection and risk assessment of oomycetes spores.

We are looking at applying ultrafiltration to make this water reuse safer. A quick and accurate analysis of the water quality is essential for our trial.

Yannah Cornelis, Researcher at Praktijkpunt Landbouw

Novel Oomycetes insights revealed by KYTOS algorithms

We put our latest KYTOS algorithm for the detection and quantification of oomycetes spores to the test. As usual, we found some very exciting things:

  • The abundance of zoospores was quantified and the water treatment efficacy could be tracked for each batch.
  • Water preparation is key. Oomycetes spores are seeded primarily at the start of the cultivation.
  • Treatments took 5 – 7 days to take significant effect.
  • Our precise zoospore quantification demonstrated that oomycetes remained highly abundant for several days.
KYTOS Oomycetes risk indicator measured during the 23 day cultivation of Chicory / Witloof.

Are you also seeking to:

  • Minimize disease risk
  • Improve water quality
  • Foster more stable production conditions
  • Promote and control microbial health

Contact us now!

Introducing WorldFish interns, Jonabel and Ngan

KYTOS is partnering with WorldFish to conduct microbiome research in carp polyculture and tilapia farming systems. Together, we want to bring KYTOS technology closer to farmers. As a precursor for further investment in this project, two interns will be reviewing the current state of knowledge. Ms. Bui Ngoc Minh Ngan will be focusing on the microbiomes of carp polyculture systems, while Ms. Johnabel Huavas will be doing the same for tilapia farming systems. Both interns are funded by WorldFish under the project, Aquaculture: Increasing income, diversifying diets and empowering women in Bangladesh and Nigeria.

Meet Jonabel and Ngan! Check out the press release here.

Jonabel Huavas

Can you tell us something more about your background?

I earned my Master’s degree in Aquaculture Major in Health Management from Ghent University in 2021 through the VLIR-UOS scholarship. I have a Bachelor’s degree in Biology Major in Microbiology from the University of the Philippines Los Baños. My interests revolve around applied microbiology, molecular biology, alternative feeds and aquaculture nutrition, microbial management, and fish physiology.

Why did the WorldFish internship appeal to you?

When I first read about the internship post, one word stood out: microbiome. During my studies, I’ve learned and became fascinated about the huge impact and application of microorganisms.  Working for WorldFish is also a great opportunity for me to learn from and work alongside aquaculture experts. The worldwide network and connection established by WorldFish is also an opportunity for me to meet and know different tilapia farmers and researchers across the world.

What are you looking to learn from the internship?

I wanted to learn about the current status of tilapia aquaculture in the perspective of microbial community management. During my graduate studies in the midst of pandemic, I was not able to do fieldwork and internship in commercial farms or other research centers. Doing this comprehensive study and networking with different stakeholders of the tilapia industry will help me learn about the current situation when it comes to microbiome management. I am also interested to learn about Kytos technology and how it can further improve aquaculture practices.

Jonabel Huavas, who will be reviewing the current state of knowledge of microbiomes in tilapia systems.

Any particular achievement you want to reach?

Being in the scientific research field, writing is inevitable. First achievement that I want to reach through this internship is to become a better writer and storyteller. Next goal in mind is to provide a tangible output that will help level up current tilapia farming systems into data-driven, microbiome-based management.

Farmers have been waiting for decades on microbiome management technologies, where do you see yourself have the biggest impact?

I see myself having the biggest impact in establishing the baseline—the current perception and appreciation towards microbiome-based management. My contribution lies into looking for the gaps between the farmers’ present understanding towards microbiome and assisting with the preparation of potential research project that will incorporate Kytos technology for best tilapia farming practices.

Bui Ngoc Minh Ngan, who will be reviewing the current state of knowledge of microbiomes in carp polyculture systems.

Bui Ngoc Minh Ngan

Can you tell us something more about your background?

I am a Master Graduate in Aquaculture at Ghent University. My research interests are in understanding the interaction of aquaculture species with their environment in order to produce healthy animals. I specialize in fish physiology, microbial community management, the host-microbiome, and microbe-microbe interactions. My objective is to work in an enriching atmosphere that promotes lifelong learning and professional growth.

Why did the WorldFish internship appeal to you?

As a graduate student in aquaculture, I want to work in a professional environment to put my acquired knowledge into practice and increase my network. WorldFish is the ideal workplace for me to start my professional career. I want to contribute and to learn how they create, advance, and translate scientific research on aquatic food systems into scalable solutions to ensure sustainability in aquaculture.

What are you looking to learn from the internship?

I am looking for opportunities to stimulate international network, extend existing knowledge, gain new insights, and learn new techniques. An internship at WorldFish would be a promising position that offers a good chance for my personal growth and contribution to the team.

Any particular achievement you want to reach?

I want to use my abilities and expertise to provide dependable and successful outcomes in the field of the microbiome in carp polyculture systems. Moreover, by working in WorldFish, I want to correct my shortcomings and upgrade my abilities to advance my career.

Farmers have been waiting for decades on microbiome management technologies, where do you see yourself have the biggest impact?

With the internship at WorldFish, my research about microbiomes in carp polyculture systems can be transformed into a series of research and practical techniques. It can help in the creation of prediction models for the microbial communities of commercial fish species to avoid invasive pathogens and improve fish health.

Ruben’s guest lecture at the 2021 German Cytometry Conference

Computational analysis of microbial flow cytometry data

DGfZ | Microbiology Session | Friday, October, 1st, 2021, 11:00am – 12:30pm

Flow cytometry (FCM) is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution. Microbial FCM data have a number of different characteristics and challenges compared to immunophenotyping FCM data. Most prokaryotic cells are much smaller in size and volume than human or mammalian cells, and although most cells are small, the size range within which microbial cells lie is larger than for mammalian cells, covering a range between 0.2 and 500µm. Microbial communities also comprise high levels of phenotypic and phylogenetic complexity (e.g. 1000s of taxa). In this talk, I will provide an overview of common pitfalls of traditional FCM computational techniques on these microbial data, and describe how we can move towards a tailored and reproducible approach for microbial ecology studies. Finally, I will list a number of open challenges to the field and offer further motivation for the use of standardized flow cytometry in microbial ecology research.