Bacteriophages (otherwise known as phages) are viruses that attack bacteria. When they recognize their specific host, they infect and subvert the cellular machinery to enable their replication. This culminates in the death of the cell and an exponential growth of the phage population in the presence of susceptible bacterial hosts.
This is a natural phenomenon, but as Damian Magill, phage team leader at IFF explained, when a business depends on making dairy products – it can be catastrophic to the bottom-line.
“My field of study has come a long way since 1935, when scientists first discovered that phages can infect starter cultures, thereby destroying dairy fermentations,” Magill said.
“Researchers immediately began investigating the way phages interacted and impacted starter strains. Ever since, scientists have worked to mitigate the negative impact that phages have on the fermented dairy industry.
“While there’s no quick fix that could entirely halt these resilient viruses, limiting the effect of phages on dairy production has been the life’s work of many biologists on our team at IFF (which was part of DuPont Nutrition and Biosciences until February 2021).”
Magill said for 40 years IFF has been collecting thousands of phages and bacterial strains from all across the globe.
“We have created a library of unparalleled biodiversity, which we believe to be one of the largest collections – if not the largest collection – of phages in the world. The viruses mostly affect Lactococci and Streptococci – forms of lactic acid bacteria – and we characterize them via genotypic and genomic analyses, as well as establishing their spectra of virulence.
“To someone in my field, just the existence of this database is extraordinary. We have characterized this biodiversity, defining the phage-host relationships and determining that strains differ by their spectrum of phage sensitivity. This collection also provides a unique spatial and temporal insight into lactic acid bacteriophages due to the decades of sampling. We not only have a lot of phages, but the fact that we have collected them over many years and from around the world provides a whole other dimension to this library.”
But Magill said the real impact of his work comes in how his team is able to leverage this diverse knowledge of phages for starter culture development.
“How we can weigh in on this perpetual arms race between phage virulence and bacterial host defense, helping the bacteria to fight back against the phages. And how we have learned to work with our customers in dairy production to develop improved phage-resistant starter culture systems,” Magill said.
One example of how the collection and observation bears fruit, is during fermentation IFF has observed some bacteria survive phage infection because they are resistant to the infecting phages. From characterizing these survivors, Magill and his team identified unique defense mechanisms to protect strains against phages.
“Once such mechanism is that of the CRISPR-Cas system, a naturally present system in bacteria that confers upon them a form of adaptive immunity against invading nucleic acids,” Magill explained.
“If a phage infects a cell containing an active CRISPR system, the cell can acquire a portion of the invading genomic material and incorporate this into an array, which is used to precisely target similar sequences and degrade them. Thus, the cell acquires immunity to other phages containing this sequence. Through the discovery and characterization of CRISPR-Cas systems, we have learned how to leverage this natural phenomenon towards the vaccination of our strains in response to an ever-changing phage landscape.”
Magill continued, “In addition to improving the phage robustness of specific strains, how we formulate and use starter cultures allows us to impose another barrier against phage impact. Phages and their hosts possess an intricate relationship such that specific bacterial strains are only susceptible to certain phages. We refer to this as their spectrum of sensitivity.
“By characterizing this, we can formulate starter cultures containing strains which have non-overlapping spectra of sensitivity. Therefore, if one strain is impacted, the others will remain untouched. By extension, the same principle can be applied to differentiate starter cultures, allowing their use to be rotated so as to prevent the buildup of phage on any one culture. In order to do all this effectively requires access to as diverse a phage collection as possible.”
He said by employing an understanding of specific resistance mechanisms, and the phage collection, the company is able to proactively increase the phage resistance of its strains.
“We apply our knowledge of phage-host relationships to design a series of starter cultures with increased phage robustness and define their use in rotation to prevent the outbreak of phage. Should phage appear, our research has shown us how to increase phage robustness and resilience.”
In addition to providing the strains at the start of a customer engagement, Magill said IFF continues to support customers by analyzing samples to anticipate potential problems that could arise and to help solve them if they do.
“Of course, total phage eradication is a Utopian fantasy. Customers should routinely disinfect and sometimes replace equipment in their production facilities – particularly when they see frequent outbreaks. But fighting phages should be a collaborative effort. We have been studying phage resistance for over four decades, and we hope that all dairy producers will benefit from the knowledge that has opened the door to unique solutions to this decades-old challenge,” Magill concluded.