The Microbial Battlefield

Cheese is abundant in bacteria, essential for its production. Cheesemakers utilize carefully curated cultures of bacteria, yeast, or fungi to create distinct cheese varieties. This microbial richness makes cheese an ideal subject for studying how bacterial communities evolve when faced with new dangers.

Among these dangers, one of the most formidable is the bacteriophage—a virus that specifically targets bacteria. Just as humans face threats from tiny pathogens, bacteria too are susceptible to disease, primarily from these bacteriophages, which resemble alien craft with their unique structures.

Bacteriophages infiltrate bacteria by injecting their viral DNA, commandeering the bacterial machinery to produce more viruses until the bacterium bursts, releasing these new viruses to find more hosts.

While the odds may seem stacked against bacteria—given the estimated number of bacteriophages on Earth (a staggering 10 nonillion)—they have developed sophisticated defenses. These include molecular weapons that they accumulate over time, similar to how hospitals stockpile antibiotics.

One notable defense mechanism is the CRISPR-Cas9 system. Initially a bacterial tool for cutting DNA, it has been adapted for gene therapy in humans. Bacteria utilize CRISPR to slice the DNA of invading bacteriophages, effectively neutralizing the viral threat before it can replicate.

The Cheese Connection: Sequencing Insights

To better understand the dynamics of bacteria in cheese, researchers sequenced the RNA of bacterial samples. This analysis revealed a wealth of viral resistance genes—17,565 innate immune systems and 1,972 CRISPR-Cas systems—highlighting the bacteria's adaptive strategies.

However, these defensive traits were not uniformly distributed; specific strains exhibited rapid gains and losses of these viral defenses. This suggests a continual adaptation process rather than a stable set of defenses. The bacteria appear to be constantly refining their CRISPR defenses, adapting to an evolving landscape of viral threats.

This insight indicates that rather than being preoccupied with any singular virus, bacteria in cheese are dynamically adjusting their defenses, illustrating the ongoing evolutionary struggle between bacteria and their viral adversaries.

Implications for Cheese Production and Health

While the notion of microbial conflict within our cheese may be unsettling, it's important to recognize that these battles are unlikely to affect human health directly. The viruses and bacteria are primarily engaged with each other, not with us.

This understanding challenges the perception of viral resistance as a static trait. Instead, it reveals a fluid and adaptive landscape where bacteria are perpetually evolving their defenses. This adaptability could also have implications for cheesemakers, particularly in developing strategies to combat harmful bacteria without compromising beneficial ones.

Research into phage therapy offers promising avenues for targeting undesirable bacteria while preserving the microbial communities that contribute to cheese's flavor and texture. In the long run, this approach could extend to improving gut health by selectively eliminating harmful microbes while maintaining a balanced microbiome.