Javad Sadeghi uses a backpack sample collectorJavad Sadeghi uses a backpack sample collector to gather water off a Lake Erie beach to filter for micro-organisms.

Analysis of microbiome provides insight into fish health

They may be microscopic in size, but microbes play a giant role in an organism’s overall health.

Javad Sadeghi (PhD 2022) spent his doctoral studies investigating the relationship between fish and the microbes that live on and in them in what is known as their microbiome. In his research, conducted in Daniel Heath’s lab in the Great Lakes Institute for Environmental Research, Dr. Sadeghi explored factors that might directly throw off the delicate balance between good and bad microbes.

“When I say microbiome, it is bacteria, viruses, fungi, and parasites — micro-organisms,” he says.

“Good ones help us digest food and help our immune system. The bad ones can cause diseases such as inflammation bowel disease or diabetes, so it is important to know which factors can change this balance making the microbiome better or worse.”

Designing a management plan to protect fish health requires first determining the factors that offset the balance of fish microbiomes.

“Knowing factors is important for ecosystem health,” says Sadeghi.

“We’re trying to determine what factors are important in fish microbiome to provide insight into factors that shape microbiome and health of the fish.”

They assessed several contributing factors, including genetics, specifically the host fish species.

“You can compare it to our understanding of why some people suffered from the COVID-19 virus, while others showed no symptoms — there are genetic factors at work,” he says.

In addition to genetics, the scientist found lake temperature and diet to be crucial factors.

“We found that diet was also a significant factor in shaping the microbiome, which is very unique, and lake temperature is a real concern because of the rising lake temperatures from climate change,” he says.

The study area included parts of Lake Ontario, Lake Erie, and the Detroit River.

“We collected 350 samples from 17 fish species at same time as we collected water samples. Not many places in Canada would have these fish species,” Sadeghi says.

Because of the unique techniques used in Dr. Heath’s lab, the fish were not harmed during the project. They collected water samples to examine the origin of the gut microbiome and swabbed the outside of the fish to determine the microbiome composition of the skin.

“You don’t need to kill them,” he says. “You take a swab and release them into the lake to know how healthy or unhealthy they are.”

Before delving into the microbiomes of fish varieties, Sadeghi assessed what factors were popping up to change the microbiome of different lakes. He says he wanted to know if fish microbiomes would be affected by the changing lake microbiomes or if they are separate.

“Some of the key findings showed the fish microbiome was different from lake microbiome,” he says.

“Imagine a fish living their whole life in a lake, all around are these bacteria, but surprisingly enough, they have a very different microbiome from the lake.”

Chapters from his PhD thesis were published in the journal, Microbiome, in the article, “Host species and Habitat Shape Fish – associated Bacterial Communities: Phylosymbiosis Between Fish and their Microbiome.”

“Knowing about these factors is important before something happens, to better respond before there is a fish health crisis” says Sadeghi.