Epigenetics Mediates Sporulation and Pathogenesis in C Diff

Many strides have been made in understanding Clostridioides difficile (C diff) in terms of its genome. However, the epigenome of C diff has not been thoroughly explored.

Investigators of a new study published in Nature Microbiology have discovered that an epigenetic process, DNA methyltransferase, mediates sporulation and pathogenesis in C diff. The discovery enhances clinical understanding of the infection and may open new avenues for developing novel treatments.

Sporulation helps C diff bacteria survive inhospitable conditions, as the vegetative form cannot survive in the presence of oxygen. The bacterium is transmitted via the fecal/oral route in the form of a metabolically dormant spore, which germinates in the intestinal environment.

Investigators deepened understanding of this process by going beyond the genetic code of the bacteria to examine chemical modifications being made to the genome. They discovered that DNA methyltransferase, which modifies gene activity without changing the sequence of a gene, is involved in the sporulation process.

"We wanted to study beyond the genetic code of the bacteria and look at what chemical modifications were being made to the genome," Gang Fang, PhD, associate professor of genetics and genomic sciences at Mount Sinai's Icahn Institute for Data Science and Genomic Technology, and senior author of the study, said in a press release.

Fang’s study team isolated C diff in fecal samples from 36 patients at Mount Sinai Hospital. Analysis showed an epigenetic pattern highly conserved through the samples. The results were then cross-checked with 300 C diff genomes from GenBank, a databank of genetic sequences maintained by the National Institutes of Health.

The GenBank genomes were found to share the gene responsible for the epigenetic pattern found in the Mount Sinai Hospital patients. The team then collaborated on 2 further studies of C diff sporulation with experts from Tufts University Medical School and the University of North Carolina, Chapel Hill.

Inactivation of the corresponding gene for DNA methyltransferase in C diff was confirmed to negatively impact sporulation in multiomics data, genetic experiments, and a mouse colonization model. Mouse models revealed that when the gene responsible for the epigenetic pattern was inhibited, as much as 100 times less bacteria was found after 6 days relative to unaltered C diff.

The study authors also noted that further experimental and transcriptomic analyses led them to believe epigenetic regulation relates to host colonization, biofilm formation, and cell length in C diff. They wrote that their study “provides a set of methods for comparative epigenomics and integrative analysis, which we expect to be broadly applicable to bacterial epigenomic studies.”

“We hope this exciting discovery will encourage further interdisciplinary collaborations to investigate epigenetics of bacteria and how we can use these new insights to develop life-saving treatments for infection,” Fang concluded in the press release.