To most people, a bucket of seawater is simply water. But to Dr. Minerva Fatimae Ventolero or simply Doc Min, a molecular biologist at the Aquaculture Research and Development Division (ARDD) of DA-NFRDI, it was home to billions of microscopic organisms that quietly sustained aquatic ecosystems.

“In the same manner as we now appreciate the role of our body’s microbiome, or microorganisms, in our overall health, microorganisms in the aquatic environment also play important functions that contribute to maintaining optimal environmental conditions that support aquatic life,” she explained.

Understanding metagenomics

Many of the solutions to challenges facing fisheries and aquaculture, from disease outbreaks to declining environmental health, could be found within these microscopic communities. This made understanding them increasingly important.

For decades, scientists studied microorganisms by growing them individually in laboratories before identifying them. While this conventional approach yielded valuable insights, it captured only a small fraction of microbial diversity because many microorganisms could not survive under laboratory conditions.

Metagenomics transformed this process. Instead of examining one microorganism at a time, it analyzed all genetic material collected directly from environmental samples such as seawater, sediments, or the gut of fish. Through DNA sequencing, scientists identified microbial communities, predicted their functions, and better understood how ecosystems worked.

According to Doc Min, metagenomics enabled researchers to identify microbial communities, predict their ecological roles, and use this information to develop potential mitigation measures for environmental challenges.

Beyond identifying species, the approach also revealed how microorganisms responded to environmental stress, interacted with one another, and contributed to nutrient cycling, waste decomposition, and overall ecosystem stability.

She found microbes fascinating because genetic information could reveal entire microbial communities invisible to the naked eye yet critical to ecosystem function. As molecular technologies advanced and DNA sequencing became more accessible, metagenomics opened opportunities to answer scientific questions that conventional methods alone could not.

Rather than replacing traditional microbiological techniques, she emphasized that metagenomics complemented them by detecting microorganisms that conventional methods were unable to culture or isolate.

In 2022, she co-authored a review published in Briefings in Bioinformatics that evaluated 20 computational tools used to identify bacterial strains from complex microbial communities. The paper served as a practical guide for researchers while highlighting the challenges of accurately reconstructing bacterial strains from metagenomic data.

Metagenomics in fisheries

Although highly technical, metagenomics had practical applications in fisheries and aquaculture.

Its greatest strength lay in detecting disease-causing microbes before they triggered large-scale outbreaks in aquaculture systems, allowing fish health experts to recommend timely interventions that could reduce production losses.

The technology also enabled scientists to monitor microbial diversity in water, sediments, and the digestive systems of cultured fish and shellfish. These data helped assess water quality, environmental conditions, nutrient cycling, and the presence of harmful microorganisms. Researchers likewise used metagenomics to monitor antibiotic resistance genes, an emerging concern for the aquaculture industry.

At DA-NFRDI, Doc Min and her team applied metagenomics to study the gut microbiome of maliputo (Caranx ignobilis), comparing farmed and wild populations. Their research examined microbial communities during larval development and identified differences between cultured and wild fish. These findings could help identify beneficial microorganisms that may improve fish survival during culture.

Challenges and opportunities

Despite its potential, metagenomics remained an emerging field in the Philippines. Advanced DNA sequencing equipment, specialized laboratories, bioinformatics software, and skilled personnel were essential, making large-scale studies both expensive and technically demanding.

Doc Min noted that greater access to training, computational resources, and sequencing technologies was needed. While institutions such as the Philippine Genome Center already provided sequencing and bioinformatics support, computational capacity for fisheries research could still be strengthened.

She believed stronger collaboration among research institutions, universities, and government agencies would accelerate the growth of molecular research in Philippine fisheries. As sequencing technologies became faster and more affordable, she envisioned metagenomics becoming a routine tool for understanding aquatic biodiversity, monitoring emerging pathogens, and improving the growth, survival, and adaptation of cultured species.

Rather than replacing conventional monitoring methods, she saw metagenomics as a complementary approach that would provide a more comprehensive understanding of aquatic ecosystems.

Inspiring the next generation

With continuing advances in genomics and molecular biology, Doc Min hoped more young scientists would pursue these emerging fields. Although genomics remained a specialized discipline in the Philippines, she believed it offered tremendous opportunities for researchers willing to embrace new challenges and continue learning.

For students still uncertain about their career paths, she shared a lesson that had guided her throughout her scientific journey: everything could be learned through dedication and perseverance.

She admitted that transitioning into metagenomics had been challenging because of its heavy computational component, an area outside her original expertise. Yet her passion for learning sustained her through the experience and reinforced the importance of curiosity, openness, and resilience in scientific research.

For Doc Min, decoding the hidden world of microorganisms was more than a scientific endeavor. It was a journey toward understanding the complex relationships that sustained life beneath the water’s surface. Through her work, these invisible connections were gradually being uncovered, providing new knowledge to support healthier aquatic ecosystems and a more resilient fisheries sector. ### (Vanessa Mae Escaño)

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References:

Coskuner-Weber, O., Alpsoy, S., Yolcu, O., Teber, E., De Marco, A., & Shumka, S. (2025). Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing. Computational Biology and Chemistry, 118, 108444. https://doi.org/10.1016/j. compbiolchem.2025.108444

Ventolero, M. F., Wang, S., Hu, H., & Li, X. (2022). Computational analyses of bacterial strains from shotgun reads. Briefings in Bioinformatics, 23(2), bbac013. https://doi.org/10.1093/bib/bbac013 

Zhang, L., Chen, F., Zeng, Z., Xu, M., Sun, F., Yang, L., … Xie, Y. (2021). Advances in metagenomics and its application in environmental microorganisms. Frontiers in Microbiology, 12, 766364. https://doi.org/10.3389/fmicb.2021.766364