What happens to a bacterial pathogen when food runs out—for several months? A new study led by Prof. Runsheng Li and Prof. Wenlong Cai using Nanopore R10.4.1 sequencing reveals that Flavobacterium columnare, a deadly aquatic pathogen responsible for columnaris disease in fish, does not change its DNA sequence during prolonged starvation. Instead, it remodels its epigenetic landscape.
The team exposed the bacterium to nutrient-depleted conditions for ten months at two different temperatures (22 °C and 28 °C). They found that while the genome remained remarkably stable, methylation patterns—chemical modifications that regulate gene activity—showed motif-specific flexibility.
"We were surprised to see that starvation did not leave a genetic scar but rather a reversible epigenetic signature," says Cai. "This suggests bacteria can 'remember' and adapt to nutrient scarcity without altering their core genetic code."
The main finding was the consistent demethylation of the specific 6mA-modified motif CAYNNNNNRTG. "Genes carrying this mark were enriched in translation and metabolic pathways—cellular processes essential for surviving long-term hunger," explains Cai. "Another motif, GCAGA, showed temperature-dependent changes, hinting at how temperature modulates starvation adaptation."
This is the first time Nanopore R10.4.1 sequencing has been applied to an aquatic bacterium for genome-wide methylation profiling. Unlike earlier methods, this technology detects multiple methylation types at single-base resolution without requiring high coverage or motif-dependent assumptions.
"Our study not only uncovers a novel epigenetic survival strategy in F. columnare but also provides a practical roadmap for bacterial epigenetics research using advanced Nanopore tools," says Li. "The findings could have direct implications for aquaculture."
Indeed, understanding how F. columnare survives starvation may help design better control strategies, such as disrupting its epigenetic adaptation or predicting outbreaks after periods of nutrient fluctuation. "The methodological framework also opens the door for similar studies in other hard-to-culture or stress-tolerant bacteria," Li adds.
