Episode Summary

Cheese rinds contain microbial communities that are relatively simple to study in the lab while offering insight into other, more complex microbial ecosystems. Rachel Dutton discusses her work studying these cheese microbiomes, one of the few microbial ecosystem types where almost all of the microorganisms are culturable.

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Julie’s Biggest Takeaways

The cheese microbiome makes a great study system because

  • The communities are relatively simple (as few as 3 different microbial species)
  • The microbial members are almost all culturable (in stark contrast to most microbial communities)

The microbes colonize the cheese rind as a biofilm, which consists of the microbes and their secreted extracellular products. Like all biofilm communities, architecture and spatial structure are important for microbial interactions on cheese rinds, as are oxygen gradations, food access, and proximity to microbial neighbors.
Rachel and her lab performed DNA sequencing on over 150 cheese samples from 10 countries to identify the microbes present on these rinds. By comparing these sequences to those they could grow in the lab (Rachel’s lab makes “in vitro” cheese medium consisting of desiccated, autoclaved cheese), they realized almost all of the organisms identified by molecular means were present in their cultures.
Does the cheese environment influence the microbial communities or do the microbial communities influence the cheese environment? Both! The pH, temperature and added salt act as knobs or dials that allow cheese makers to fine tune the final cheese product.
Rachel was inspired to work on cheese after taking the Microbial Diversity course at Woods Hole, where the students spent a lot of time looking at the beautiful but complex interactions within microbial mats. Upon cutting open some Tomme de Savoie from a French colleague, she noted similarities between the microbial mat and the layered cheese rind

Featured Quotes

“The biofilm that colonizes the surface of the cheese has a lot to do with how the cheese ends up looking and smelling and tasting, and we actually eat this biofilm when we eat the cheese.”
“We’re able to see that of all of the things that we identified by reasonable sequence abundance, we could also find them in culture. This told us that we were able to get a lot of these microbes in culture, which is not really possible in microbial ecosystems, but is one of the really strong advantages of working in the fermented food community.”
“We’re looking at these interactions because they’re happening on cheese and we can study them in the lab but they are things that are happening broadly across ecosystems, which I think is very exciting.”
“We’ve done some work on the succession of species over time. You have these very very reproducible successions over time, even though a lot of these cheeses are not inoculated with specific species; these are species that are coming in from the environment but they’re very reproducible communities. There are some beautiful dynamics that happen and we’re starting to look at the interactions between species that may be driving some of these dynamics.”
“We have this big need for model systems. One of the things I hope is that we’ll have more people developing simple model systems for microbial ecology so we can compare results and see what the general principles are.”

Links for This Episode

History of Micobiology Tidbit

Rachel gave 2 examples of Penicillium species that affect cheese characteristics, but I was also thinking about the antagonistic interactions that Penicillium species are likely having with the bacteria that co-colonize the cheeses – after all, one of the most famous discoveries of the 20th century was the zone of exclusion surrounding Penicillium notatum that contaminated Alexander Fleming’s bacterial plates.
So in that spirit, in today’s History of Microbiology tidbit, I’d like to revisit that era of antibiotic discovery, but rather than highlight Fleming’s discovery, I want to highlight the work of a scientific team to improve upon this discovery. The United States Department of Agriculture opened the Northern Regional Research Laboratory or NRRL in Peoria, Illinois in the 1940s after Fleming’s 1929 publication of the effects of penicillin on bacterial growth. The scientists within the Fermentation Division at the NRRL were addressing 2 major problems in the Penicillium isolates that had been cultured thus far: first, the strains grew best on solid agar, which complicated the collection of their secreted penicillin compounds, and second, the concentrations of penicillin produced by these strains was very low, meaning that a lot of fungus had to be grown – on plates – in order to produce a small amount of effective compound. Neither of these are great qualities for mass production.
The team consisted of a number of scientists, and included a technician named Mary Hart, who later became known as “Mouldy Mary.” Hart was charged with finding better Penicillium strains that could more effectively inhibit Staphylococcus growth using the zone of inhibition assays that we still know today. She turned to crowd-sourcing Penicillium strains from the local Peoria community, which is where her nickname originates. In addition to picking through fruit and vegetable stands, looking for older produce, she would also speak with managers to find out if there were any rotten items in the back that were deemed unfit for sale. She eventually found what she was looking for on a canteloup with a fuzzy growth on its navel. Hart was quoted saying she knew this cantaloup mold would be the one: “I remember when I got that Texas cantaloup, it proved to be ‘The One!’”

A strain that secreted more drug would be expected to have a larger zone of inhibition, where the bacteria couldn’t grow, surrounding the fungal colony. By screening 241 Penicillium isolates, Hart found that the mould from the canteloup - mould number 72 - secreted about 200 times the amount of penicillin as Fleming’s original isolate. With x-ray induced randomized mutagenesis, Hart and the researchers were able to increase this to a 1000-fold increase from the original isolate. The canteloup mold, Penicillium chrysogenum, is the progenitor strain of all penicillin-generating strains used today. Fun fact: after cutting off the mold, Hart passed around cut up pieces of the cantaloup as a snack for her coworkers.

Simultaneously, Hart’s boss, Andrew Moyer, was at work to improve the yield of a submerged fungus grown in fermentative conditions, rather than surface-dwelling moulds. One of the advantages to working in Peoria was a local corn starch factory that produced corn steep liquor as a byproduct. This corn steep liquor was normally dumped into the Illinois River, but Moyer’s team tried adding it to the fungal medium. This addition, according to another research team member, Robert Coghill, this was a turning point in their research: the addition of this corn steep liquor “increased the yield 20 times and no other lab in the United States used this product.”

The combination of a new Penicillium strain and the means by which to grow it in fermentative culture facilitated the mass production by 15 pharmaceutical companies to produce 14,000 pounds of penicillin. Remember, this is all happening during World War II, and the antibiotic produced by these facilities were vital to treating battlefield wounds and infections.

I love this story because it highlights the importance of all members of a scientific team and because it shows that major discoveries are not transformative without the iterative work of many players to refine and build upon the initial observation. Many associate Fleming with the discovery of penicillin, but Moyer, Coghill, and Hart played important roles in developing the fungal compound into an applicable drug.

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