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Microbial mystery: The invisible network protecting the whale shark

In the vast expanse of the world’s oceans, the largest fish – the whale shark – is facing challenges that extend far beyond what the eye can see. 

While the threats of habitat loss and human activities such as fishing and shipping are well understood, a new study unveils a less explored dimension of marine conservation – the microbial health of the whale shark.

Researchers at Flinders University in South Australia, along with a collaboration of 12 international institutions, have made major progress in understanding the role of diverse microbial communities that reside on the skin and tissue of these endangered sharks. 

New marine microbes discovered

The study describes new marine microbes for the first time, marking an essential step toward understanding this crucial aspect of the marine ecosystem.

Dr. Michael Doane, a researcher from the Flinders Accelerator for Microbiome Exploration (FAME) group, said the research is the most extensive microbiome study to date of a wild marine animal of this physical size. 

A balanced network 

“While microbial species differ across the world, they work together to form a balanced network that contributes to the health of the sharks,” said Dr. Doane.

“It is important to measure and analyse the distinct and diverse epidermal microbiome of the global whale shark populations to work towards understanding how the microbes affect the wellbeing and survival of this amazing animal.”

“The characteristics of a balanced microbial community are not well described for any species, but especially for sharks, which form a vital link in ocean foodchains and ecosystems.”

Focus of the study

The study involved 74 whale sharks in the three major ocean basins, and will form a baseline for future analysis and highlight how microbial species differ around the world.

By using cutting-edge genomic sequencing technology, the scientists were able to collect microbial samples from five renowned diving sites, including Ningaloo Reef in Western Australia, Oslob in the Philippines, Mafia Island in Tanzania, and La Paz and Cancún in Mexico. 

Complex interplay 

The delicate balance of microbial communities on the skin surface is not well understood, particularly in sharks. This balance is pivotal for the health and survival of the whale shark, a key player in ocean food chains and ecosystems. 

The findings reveal a complex interplay between microbes and their host, the whale shark.

“The microbes form a complex network pattern on the skin surface, which is consistent across sharks from each location, revealing characteristics of what comprises a balanced or unbalanced microbiome,” explained Dr. Doane.

What the researchers discovered 

Using mathematical modeling, the team explored the interactions between the microbes to comprehend how they form a network or community. 

Remarkably, the experts identified 34 new species of microbes, with the highest number of novel microbial species found in the whale sharks from Ningaloo.

Striking the right balance

Flinders University Professor Elizabeth Dinsdale is a co-author of the study published in Scientific Reports. She noted that the right balance of microbes are critical to the well-being and survival of the host with which they live.  

“In humans, for example, skin microbes are always present, and when these communities are ‘healthy,’ they go unnoticed; however, when they are unbalanced, they cause skin conditions such as dermatitis, or skin infections,” said Professor Dinsdale.

“As microbes are too small to see, it is important to gain an understanding of how these complex network patterns fit together for a healthy microbiome balance. Unbalanced interactions can lead to a loss of benefits for the host and can result in disease.”

Study implications 

“We now have a baseline for the healthy microbiome of whale sharks, which can be used to monitor the health of the whale shark and we also developed a non-invasive method to identify the effectiveness of conservation strategies.”

More about whale sharks

Whale sharks (Rhincodon typus) are fascinating creatures that can grow up to 40 feet long, while most average around 18 to 32.8 feet. 


The whale shark has a distinctive appearance, with a broad, flat head, two small eyes at the front of its head, and a pattern of white spots and stripes over a dark blue or brownish back.


Despite their massive size, whale sharks primarily eat plankton, including krill, copepods, and small fish. They are filter feeders, swimming with their mouths open to collect food in their gill rakers.


Whale sharks can be found in warm oceans around the world. They are known to migrate thousands of miles to find food and to reproduce. Notable places where they are frequently observed include the coasts of Australia, Belize, the Maldives, Mexico, and the Philippines.


Whale sharks are ovoviviparous, which means they give birth to live young. A female can give birth to several dozen to over 300 pups in one litter. Pups are around 16 to 24 inches (40 to 60 cm) long at birth. They have a long lifespan, living up to 70 years or possibly even more.

In an era where marine conservation is paramount, the intricate relationship between the whale shark and its microbiome presents a fresh perspective. The Flinders study not only unlocks a new dimension in the understanding of these magnificent creatures but also underscores the interdependence of life within our oceans.


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