IFF Food Biosciences has managed to map the entire immune system of Streptococcus thermophilus – one of the most widely used bacteria in dairy fermentation – to better understand its 28 defense systems, including three unique CRISPR systems. By integrating many of these defenses into the bacteria’s native genome, they created a synergistic shield that blocks phage attacks without compromising milk acidification or bacterial growth – essentially hacking evolution to protect these microbial heroes that do so much for our cheese and yogurt. IDM spoke with Dennis Romero and Damian Magill from IFF Food Biosciences about their findings.
IDM: Dairy cultures are sensitive to bacteriophages, till now the industry uses culture rotation at a quite high expense. Do you think that dairy cultures can be made immune to phages one day?
Romero: If I may clarify the first statement, “culture rotation” is indeed a key strategy the industry employs to address bacteriophages; something that has been practiced for decades, as elaborated below. This practice will likely continue being used in the foreseeable future, despite new recently discovered technologies. The “high expense” should be put into context as the dairy processor does not necessarily realize this cost.
Regarding the question, consider human vaccinations as an example. As with influenza and now Covid, a person can be vaccinated against the current virus that’s prevalent at a given time. It’s the same with dairy cultures in that we can introduce a specific phage defense system (vaccination) against the current phages in the industrial dairy environment. However, given the opportunity (a susceptible host) and time, the phage will adapt and mutate to overcome the defensive system. This is what’s happening with influenza and Covid; the virus mutates and people need to be vaccinated against the new viral variants.
The rotation scheme employed by the dairy industry effectively reduces the opportunity for phages to mutate by reducing the time a susceptible host is exposed to a given phage.
Magill: I am going to answer the question in regards purely to eliminating the phage problem, factoring in more than just rotation in this strategy. I believe that as long as we rely on life in its natural form to drive our industrial processes, we will continue to face the various challenges that come with it. Perhaps one day the use of purely synthetic organisms will remove all disadvantages and allow for precision fermentation, but the surprises that come with using natural organisms have allowed us to discover new functionalities, bringing unique products to our customers. It would be bold to assume that in a matter of 100 years we can completely eliminate what has arisen over the course of billions of years of evolution, but the application of multilayered strategy including rotation and use of bacteriophage insensitive mutants allows us to effectively manage the phage problem.
IDM: What is your concept for making S. thermophilus more stable against bacteriophages?
Romero: Interaction between host (S. thermophilius) and bacteriophages has been ongoing since the beginning of time. To survive a phage infection, S. thermophilus had to develop a resistance (defense system) to that phage. Our work has shown the diversity of defensive systems that have naturally arisen. Conversely, for the phage to survive, it must find a way to overcome those host defenses. The pressure is quite strong – adapt or cease to exist. This interplay between host and phage will continue as long as both exist in the same environment.
Our research has been directed towards discovering the myriad ways S. thermophiluis has evolved to protect itself against phage infection; the presence of these systems varying between starter culture strains – hence one potential reason for their phage sensitivity. By identifying and characterizing these defensive systems, they can be introduced into the phage sensitive strains – similar to a vaccination – thereby protecting them against phage attack.
Magill: I agree with Dennis on the core principle of understanding the phage host relationship and steering it in our favour. This is exemplified by the use of naturally occurring defense mechanisms as a means of vaccination. Referring back to the concept of rotation and construction of multi strain starter cultures, these are built so no phage overlaps exist between components; something determined by lysotyping strains. A strain’s lysotype is the permissibility of that strain to be infected by certain phages and is a complex product of recognition factors and defense mechanisms. This falls under the spectrum of the phage-host relationship and is ingrained in everything that we do. Understanding this relationship gives us multiple tools towards managing the phage problem.
IDM: Is it some kind of genetic modification?
Romero: Strictly speaking, genetic modification is defined as any change in the genome of a living organism. Even a single change in the roughly 2,000,000 nucleotides in a typical S. thermophilus genome would be a genetic modification.
Hence, introducing a phage defensive system from one strain into a strain that was lacking that system would be a genetic modification by the strict definition. It should be noted that the presence or absence of any of the phage defensive systems naturally occurring S. thermophilus varies between strains and is a consequence of a particular strain encountering a particular phage and surviving.
Magill: I presume the question refers to the development of GM constructs, to which the answer is no. As Dennis states, these are naturally occurring defense systems that are distributed in various manners across strains. The presence, absence, and abundance of these reflect the local phage landscape of a given strain and, indeed, diversity amongst a population of different strains, which allows for a certain plasticity in the immune profiles present. Characterising these systems and transferring them via natural non-GMO approaches allows for a targeted approach towards immunizing our strains in response to a dynamic phage landscape.
IDM: If so, how do you think consumer acceptance can be assured?
Romero: I think that once properly explained, the consumer will be accepting starter strains made immune to phages. As mentioned, the defensive systems occur naturally in S. thermophilus strains that have survived phage infections; our work is transferring those systems between strains. In nature, such an exchange could happen under normal conditions, such as from exposure to a bacteriophage attack.
Magill: We speak not of GMO organisms but of naturally occurring systems. Even customers using artisanal undefined starter cultures are using strains containing defense mechanisms such as these against phages. Our research is focused on the discovery and understanding of these mechanisms so that we can best apply them (but in a sense, as alluded to by Dennis, this is already occuring). A natural parallel can be made between the processes of natural selection and selection by humans. Nature provides variability, and we steer it in the desired direction. This could be considered an extension of that and, as such, should be readily acceptable.
IDM: Do you work with more culture organisms or do you target only yogurt bacteria?
Romero: We work with many culture organisms. For fermented foods (such as yogurt, cheese, kefir, sour dough, pickles, salami, etc.), the majority of these organisms fall into a class of microbes called Lactic Acid Bacteria (LAB). As their name implies, LABs ferment sugar into lactic acid, which acts as a preservative, inhibiting spoilage and pathogenic bacteria, while also imparting texture and flavor to the fermented food. S. thermophilus, along with the closely related Lactococcus species, are amongst the most commonly used LABs for food fermentations.
Photos: IFF Food Biosciences
