Using the roundworm C. elegans as a "living test tube," researchers at the University of Florida have identified specific gut bacteria that promoted protein misfolding throughout the body, as well as others that were protective.
The findings, published in the May 6, 2021, issue of PLoS Pathogens, give new insights into the role of the gut microbiome in neurodegeneration and muscular disorders.
Senior author Daniel Czyz, an assistant professor at the University of Florida's Institute of Food and Agricultural Sciences, told BioWorld Science that that in addition to its specific findings, the paper illustrates the strengths of very simple model organisms to break down complex bacterial communities into manageable parts.
The gut microbiome has long been linked to the health of other organs, including the brain. But "a lot of the studies in humans are correlational," he said.
Because the individual members of the microbiome influence each other, identifying which specific bacterium or metabolite is causal for a health effect is extremely challenging. Mouse models, too, are simpler but not simple enough to avoid the issue altogether.
C elegans, though, has fewer than a thousand somatic cells -- 959, to be exact. About a third of those cells are intestinal cells, and the animal sports 123 muscle cells. At the same time, the animal's body plan is similar, in its extremely simplified way, to that of humans.
The worms that Czyz and his colleagues used for their work are engineered to express a polyglutamine stretch attached to a sensor that enabled them to detect aggregates of misfolded proteins. Glutamine repeat expansions underlie Huntington's disease as well as several dozen other disorders, collectively known as the polyglutamine or polyQ disorders.
By colonizing the worms with one gut bacterium at a time, they were able to identify species that increased the misfolding of the polyglutamine-containing proteins not just in the gut, but also in the animals' 123 muscle and 302 brain cells, suggesting that "bacteria may secrete something that affects the host in a way that enhances or disrupts protein folding across tissues," Czyz said. "That's when it got really interesting."
Unexpectedly, the team also found that the offspring of colonized C. elegans, which were not colonized themselves, also showed increased misfolding. Czyz and his colleagues originally suspected an epigenetic effect, but "at this point, we don't think it's epigenetics, because the second generation loses that [effect]," Czyz said. Instead, he suspects that the aggregates also occur in germline cells and affect offspring via effects on the germline.
The team also identified several species that were able to reduce misfolded protein aggregates. Two different Prevotella species in particular, P. disiens and P. corporis, "almost completely suppressed protein aggregation."
Both those Prevotella species secrete butyrate, a short chain fatty acid that is one of the major metabolites produced by health-associated gut microbiome bacteria.
They also showed that "If we supplement worms' butyrate, that suppresses the negative effect that the bacteria have on protein folding," Czyz said.
When the team colonized C. elegans with an Escherichia coli species that had been engineered to product butyrate, it suppressed protein misfolding and aggregation in the colonized worms.
And when they co-colonized C. elegans with helpful and harmful bacteria, the engineered E. coli was able to suppress the negative effect of detrimental bacteria.
A link to antimicrobial resistance?
Czyz and his colleagues are also interested in antimicrobial resistance (AMR), a looming public health crisis that Czyz sees as related to protein misfolding disorders.
"Almost all of the bacteria we found associated with protein misfolding are also associated with antibiotic-resistant infections," he pointed out. Two of the bacteria that had the strongest detrimental effects were the bacteria Pseudomonas aeruginosa, Klebsiella pneumoniae, both ESKAPE pathogens that the Infectious Disease Society of America considers the most urgent public health threats due to their extensive drug resistance.
Czyz has a two-hit hypothesis with respect to the development on neurodegeneration, where individuals who are predisposed to neurodegenerative diseases by carrying a protein-destabilizing mutation in their proteome will develop outright illness if they are also colonized with bacteria that increase protein misfolding.