Microbial diversity and ‘unique’ cheeses

Posted on March 22, 2016   by Yufan Chen

Traditional cheese-making with raw milk utilises bacteria from the local environment. Today at the Annual Conference, Bronwen Percival, Technical Manager at London-based Neal’s Yard Dairy, will explain how this traditional way of producing cheese is making a comeback, but how modern molecular microbiology is arming artisan cheesemakers with more knowledge than ever before.

Cheese, in various forms and flavours, is a staple of many diets around the world and its origins date back thousands of years. Cheese can be made in lots of different ways; many commercially available cheeses are made with pasteurised milk – a process that eliminates pathogens that could spoil the milk – but cheese can also be made with unpasteurised milk. Comté, for example – made in the Franche-Comté region of France – uses raw milk from grass-grazing cows and was historically made by farmers living in the mountains who left the cheese to mature while they tended their livestock.

Nowadays, most factory-made, pasteurised cheeses use ‘starter’ cultures, which are added during the cheese-making process to standardise flavours and maximise production. Often these cultures are from the Lactococcus or Lactobacillus genera of bacteria. Controlling the starter cultures used ensures that the blocks of cheese you pick up from supermarket shelves will taste exactly how you expect.

Conversely, the microbial communities in raw milk are very varied, and raw milk cheesemakers are becoming increasingly interested in the microbes present in their cheeses to help them find out what is making their products taste good, or not so good. Bronwen explains that a conference organised by Neal’s Yard Dairy in 2012 highlighted the decreasing microbial diversity in raw milk due to the focus on hygiene. Milk producers have been working for many years to lower the total bacterial count of their milk because of the widely-held idea that less bacteria equals better milk. “The result was that [the cheesemakers] were wiping out the character of the milk,” she says. This spurred her to look into specific studies on the microbial communities present in cheese, and working together with cheesemakers and scientists to utilise this new information. “It’s not about making cheese with more microbes, it’s about working more intelligently with our microbial resources to make cheeses that are more interesting and unique.”

Traditionally, cheese types were tied to where they were made, with each location providing a distinct climate and microbial population, which lead to a distinctive cheese. New research and technologies, such as high throughput DNA sequencing, are beginning to give modern artisan cheesemakers the opportunity to identify the microbial communities present on their individual farms. “People are hoping to discover the mechanisms, such as less-chemical-intensive teat cleaning methods, that will help them to go from simply producing raw milk cheese, to actively understanding where the microbes are coming from on their farm,” says Bronwen. “We want to be able to make cheese in a way that highlights the unique flavours of each farm.”

In a project that spanned from 2009 to 2014, researchers at Harvard University studied the formation of the microbial communities on cheese rinds, looking at how the different microbes found there interact. Although the work was not implicitly undertaken to inform cheesemakers, it was keenly anticipated by the cheese community: “It suggested that as technology becomes cheaper and more accessible at a practical level, there could be opportunities where [cheesemakers] could take samples of their milk at different times of the year and look at how the diversity of the microbes is changing,” Bronwen explains.

But it’s not just a case of producing ‘interesting’ cheeses; starter cultures with lower diversity are susceptible to attack by bacteriophages. A bacteriophage, or just phage, is a virus that infects and can kill bacteria. Phages are usually specific to a narrow range of bacteria and can often survive the pasteurisation process, so the lack of diversity in starter cultures means that the presence of phages can easily spoil multiple batches of cheese. To combat this, many industrial factories have to select and use combinations of different strains to prevent an attack that kills all the bacteria needed to sour the milk.

Because of their complexity, cheeses made with natural starters are at a lower risk of having their entire bacteria community demolished through phage attack – any present phages may only kill off a few strains, and the remaining bacteria can continue their job of souring the milk. However, this inherently means that there is less standardisation in the cheese produced. For a traditional raw milk cheesemaker, it makes sense to allow the natural bacteria prevalent around their farm to be involved in the production, even if it means the flavour isn’t identical each time. Bronwen says that, at Neal’s Yard Dairy, they acknowledge that each batch will taste different: “But as long as they have a good flavour, it doesn’t matter… As long as they can control what’s going on in their milk and [the process] in a way that gives a consistently delicious and high-quality product, it’s all for the better if it’s changing every day.”