THOR study herds complex microbiomes into a model for improving them

15 Mar 2019 --- Although the use of probiotics for gut health has proliferated among consumers, the complexity of these microbes and the microbiome can leave researchers unsure of how to produce predictable and long-lasting changes for the better. New research from the University of Wisconsin-Madison hopes to address this complexity through the development of a microbe community named THOR which should enable the researchers to understand the microbiome better by investigating the close relationships between strains, for example.

The THOR community is made up of three species of bacteria isolated from soybean roots and grown in the same environment. Each of the three members of THOR has a sequenced genome, and an array of tools are available to easily study the bacteria in isolation and together. This opens up opportunities to unravel the complexity of microbial communities such as THOR and others, according to the study. A better understanding of these microbiomes could help scientists figure out how to improve them.

The complex community of microbes in THOR developed new behaviors together that couldn’t be predicted from the individual members alone – they grew tougher structures known as biofilms, changed how they moved across their environment and controlled the release of a novel antibiotic.

Combined, the members of THOR boasted some 15,000 genes and were capable of producing thousands of small molecules, creating “layers of complexity” over time and across space, says Jo Handelsman, Director of the Wisconsin Institute for Discovery at the University of Wisconsin-Madison.

The members of the community have been coined “The Hitchhikers Of the Rhizosphere” by the researchers. This is because in previous studies the team noticed that several bacteria “came along for the ride” when members of common Bacillus bacteria were isolated from the microbiome of soybean roots, known as the rhizosphere. These “hitchhikers” only showed themselves when Bacillus bacteria were grown in the cold for several weeks.

Those close associations between different species suggest they could serve as a model community to test how complex traits emerge when multiple species share the same space. The researchers settled on species from the Pseudomonas and Flavobacterium groups of bacteria to grow and study alongside Bacillus.

When grown alone, the Pseudomonas member of THOR produces a biofilm, a hearty structure that protects the bacteria from its environment. Biofilms gum up implants used in medicine and make bacteria resistant to antibiotics. When all three members of THOR were grown together, the community produced two times as much biofilm and the biofilm lasted longer than when Pseudomonas was alone, the researchers explain.

“Even when their populations are small, these other species are sparking larger biofilms,” says Handelsman.

Other complex traits emerged in THOR as well. The Bacillus member reduced the production of antibiotics made by Pseudomonas, protecting Flavobacterium from their effects. And the other members of THOR induced Bacillus colonies to grow out like the branches of a tree, spreading over and around the other bacteria in complex patterns.

Many efforts to manipulate microbiomes are focused on improving human health, and model communities like THOR could help scientists understand how complex microbial relationships can be altered to benefit health

THOR’s information about the microbiome of plant roots, the rhizosphere, is just as vital, the researchers add. The rhizosphere helps glue soil together, preventing erosion. And soil locks up three times more carbon than floats in the atmosphere, making it an important element in addressing climate change. Knowing how individual microbes come together to produce the rich, complex behavior of the soil microbiome may be a key to maximizing the benefit we derive from these unseen communities.

NPD in the gut-health space is surging as consumer knowledge and microbiome investigations increase.

In an example of the connection between NPD and clinical findings, Yakult recently launched a new synbiotic drink to the South Korean market, enriched with MicrobiomeX – an active flavonoid ingredient developed by BioActor, an ingredients company which develops health ingredients for healthy aging and active living. The company’s foray into the flavonoid space for gut health marks “a first for the microbiome space,” Hans van der Saag, CEO and Founder of BioActor, tells NutritionInsight.