Researchers say studying host organisms and their microbes together could lead to better understanding of diseases and agricultural output

Traditionally, when researchers focus on plants and animals, they study them in insolation, away from their microbiomes, those complex communities of microorganisms like bacteria, fungi and viruses that live on, in and around all organisms.

Now, an international team of scientists — including Antonino Malacrino, an assistant professor in Clemson University’s Department of Biological Sciences — say it’s time for a paradigm shift.

They say hosts and their microbiomes form a single system, called a holobiont, containing genetic information from both host and microbial genes, together known as a hologenome. The combined genome has been shown to significantly impact the traits and health of the host organism, they say.

Studying the interaction between host organisms and microbes could lead to a better understanding of disease, improve food production and mitigate the effects of climate change, they say.

“We have to change the approach to really understand how life works,” said Malacrino, a part of The Holobiont Biology Network, which includes faculty from various universities.

The researchers presented their insights in an article published in the journal Science titled, “The disciplinary matrix of holobiont biology.”

Symbiosis

Malacrino said the symbiosis between animal and plant hosts and their microbiomes affects fundamental biological functions such as growth, pathogen resistance and adaptation to environmental stresses.

The researchers said holobiont biology shows that microbiomes often have a significant influence on traits previously attributed to the host genome alone. The hologenome — the combination of the host and microbiome genomes — has proven in various scientific studies to be a more effective predictor compared to the analysis of the genome alone for several traits.

“There are times that disease cannot just be explained by the host genome or just by the microbiome genomes, but both of them together,” Malacrino said. “Looking at them both together allows us to understand the interdependence between the host and its microbiome.”

New diseases

Malacrino said scientists all over the world are observing new diseases in plants from both unknown pathogens and pathogens that have been managed in the past. He said scientists, in some instances, are not able to associate one pathogen to the new disease, which makes their management extremely difficult. However, considering the host and microbiome as a unit could explain how new diseases occur, he said.

“It’s an imbalance within the microbiome and an imbalance between the host and the microbiome. This unbalance gives space to weak pathogens that normally aren’t a problem to cause a disease. What can cause this imbalance often is climate change. Climate changes can alter the balance between the host and the microbiome and between microbes within the microbiome,” Malacrino said.

New solutions

Malacrino said by understanding the holobiont, researchers can provide new solutions for handling these diseases.

“In the case of plants, we can find a sustainable solution that is microbiome-based that won’t harm the environment,” he said. “We have two fights that go together. One is the fight against food scarcity and the other one is the challenge of climate change. And we want to fight both of them without harming the environment. Using the microbiome and its connection with the host could be one of the ways we look at the future of agriculture.”