The germination switch: a single amino acid drives host adaptation in Clostridioides difficile
Oeiras, 22nd of July 2026
The bacteria Clostridioides difficile (C. difficile) is amongst the leading cause of diarrhea associated with antibiotic therapies worldwide. It is responsible for hundreds of thousands of infections each year and, while commonly associated with hospitals, studies show that most transmission occurs in the community, prior to hospitalization.
A new study by a team of ITQB NOVA researchers, of the Microbial Development Lab, have uncovered a substitution that can explain how C. difficile easily adapts to different hosts. This discovery, published in Environmental Microbiology, can have important implications in future research on disease prevention.
C. difficile can reside in the gut as spores without causing disease. However, antibiotic use can disrupt the gut microbiota, leading to dysbiosis and alterations in the bile salt pool. These changes promote the germination of C. difficile spores and its subsequent growth, which can result in colon inflammation, diarrhea, and even more serious complications, such as bowel perforation or death. But little is known about how these bacteria adapt to different hosts, especially considering the differences in the bile and gut microbiome.
The study led by Isabel Roseiro, PhD student at the Microbial Development Lab, focused on strains of C. difficile commonly found in animals and other environmental sources. “We combined microbiology, genetics, biochemistry, genomic epidemiology, and protein structural modelling in a multidisciplinary approach”, explains Isabel, “and found that a single amino acid substitution in a protein of C. difficile is key to the germination process in response to lower concentrations of bile salts and acids.”
This is a natural occurring change, which can help explain how C. difficile adapts its machinery to the different environments encountered in different hosts. “We showed that these spores can germinate in response to bile acids that are characteristic of each host. This substitution also broadens the spectrum of bile salts capable of triggering germination, including bile salts previously thought to be inhibitory and that are particularly abundant in animals such as cattle and pigs. This may increase persistence in agricultural settings and increase opportunities for transmission between animals and humans”, emphasizes Adriano O. Henriques, leader of the lab.
“Since spore germination is required for infection, understanding its regulation may help identify strategies to prevent disease”, adds Mónica Serrano, auxiliary researcher of the same lab. She concludes, “overall, these findings support a One Health perspective, highlighting the interconnection of human, animal, and environmental health.”
The next steps entail a better understanding of the molecular mechanisms underlying C. difficile spore germination, particularly how germination signals are detected and transmitted through the germination machinery.
This work was done in collaboration with Mónica Oleastro Lab (National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Portugal) and Søren Persson (Statens Serum Institut, Denmark). This project was funded by Fundação para a Ciência e Tecnologia.
Original Paper:
Environmental Microbiology | https://doi.org/10.1111/1462-2920.70332
A Single Amino Acid Substitution in CspA Increases Germination Sensitivity and Broadens Bile Salt Germinant Specificity in Clostridioides difficile Spores
Authors: Isabel Roseiro, Alexandra Nunes, Diogo Martins, Frederico Alves, Søren Persson, Adriano O. Henriques, Mónica Oleastro, Mónica Serrano
