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Researchers Identify Three General Types Of Microbial Communities That Live On Cheese

After studying 137 varieties of cheese collected in 10 different countries, including the US, researchers at Harvard University here have been able to identify three general types of microbial communities that live on cheese.

The research opens the door to using each as a “model” community for the study of whether and how various microbes and fungi compete or cooperate as they form communities, what molecules may be involved in the process and what mechanisms may be involved.

The study, which is described in a July 17 paper in the journal Cell, was written by Benjamin E. Wolfe, Julie E. Button, Marcela Santarelli and Rachel J. Dutton of Harvard’s FAS Center for Systems Biology.

“We often use model organisms like E. coli or C. elegans because they can give us an understanding of the basic mechanisms and principles of how biology works,” Dutton noted.

“The goal of this work was to identify something like a model organism, but for microbial communities; something we can bring into the lab and easily replicate and manipulate.”

“The challenge in studying these communities is that many of the environments where they are found, such as the human body or the soil, are hard to replicate because they’re so complicated,” Dutton continued.

“Cheese seemed to offer a system...in which we knew exactly what these communities were growing on, so we thought we should be able to replicate that environment in the lab,” Dutton said.

Microbial Diversity Of Rinds
In the production of traditionally aged cheeses, a rind forms on the surface of the cheese as it ages. Previous research has provided a preliminary view of the microbial diversity of rinds from a limited number of artisan cheeses; these rinds are composed of a collection of bacterial and fungal species that come from raw milk, starter cultures added by the cheese makers, the aging environment and, in some cases, unknown sources.

Because cheesemaking spans continents and encompasses a variety of cheese styles, widespread sampling of in situ patterns of rind microbial diversity could reveal major factors influencing rind community formation across geographic and environmental gradients, the researchers explained.

They used PCR-based amplicon sequencing to characterize the bacterial and fungal diversity of 137 different cheeses made in 10 different countries across Europe and the US.

Across all communities sampled, only 14 bacterial and 10 fungal genera were found at greater than 1 percent average abundance. The number of these dominant genera per sample is on average 6.5 bacterial genera and 3.2 fungal genera.

Given the dominance of a limited number of genera, it might be expected that the majority of the community would originate from starter cultures, the researchers noted. However, on average across all samples, they found that at least 60 percent of the bacteria and 25 percent of the fungi present are not starter cultures and therefore orginate from environmental sources.

For most uninoculated microbial groups, their function in the context of the community or in the production of cheese is largely unexplored. For example, the researchers identified two bacterial genera, Yaniella and Nocardiopsis, that have never been reported in food microbial ecosystems.

Many of the 24 dominant genera that the researchers identified are widely distributed across the samples, but their abundance within each rind community is variable.

This divergence in community composition is best explained by the rind type of the cheese (washed, bloomy, and natural), whereas country of origin, milk treatment, or milk source are only weakly associated with community divergence.

These three rind types are a result of three main approaches to aging cheese. Bloomy rind cheeses, such as Brie and Camembert, are heavily inoculated with fungi to create a dense rind that is usually white in appearance.

Natural rind cheeses, such as clothbound Cheddars, St. Nectaire, and Tomme de Savoie, are largely untouched during aging.

And washed rind cheeses, such as Taleggio, Gruyere, and Epoisses, are initially produced in a manner similar to bloomy or natural rind cheeses but are then washed repeatedly during aging with a salt solution.

The hybridization of styles in washed rind cheese aging may explain why the composition of these cheeses is interpersed throughout the bloomy and natural rind communities.

Geography vs. Environment
If the microbes that colonize rind communities are dispersal-limited, diversity could be shaped in part by stochastic processes; cheeses made and aged in the same geographic regions would have more similar community composition than those aged farther apart. However, across the researchers’ entire data set for Europe and the US, community composition is not significantly correlated with geographic distance.

“What we ended up finding is there are microbes which occur in all the areas where cheese is made,” Dutton said. “What was interesting is if you make the same type of cheese in France or in Vermont, they will have very similar communities.”

In contrast to a limited role for geography, environmental conditions do correlate with variation in community composition, the researchers found. During the process of aging cheeses, surface moisture, pH, and salinity are carefully controlled, and some of these variables are significantly different across the three rind types.

The researchers found that moisture is the best predictor of rind community composition. The fungus Galactomyces and four genera of Proteobacteria, both found in high abundance on moist bloomy rinds, are positively correlated with moisture, whereas several other fungal and bacterial taxa (Scopulariopsis, Aspergillus, Actinobacteria, and Staphylococcus), which are abundant on dry natural rinds, are negatively associated with moisture.

Abiotic conditions have a strong influence on rind community diversity, but interactions among microbes could also play a role. Researchers used their independent bacterial and fungal amplicon data sets to quantify co-occurrence patterns across individual bacterial and fungal genera and found evidence for both strong positive and negative associations. These could be explained by interactions among species and/or shared environmental niches.

The researchers’ work presents cheese rind microbial communities as an experimentally tractable system for exploring fundamental questions about how microbial communities assemble and function.

Rind communities are widespread and accessible, and the researchers’ in situ work shows that reproducible communities of bacteria and fungi form in geographically distant parts of the world.

“Our in vitro experiments demonstrate that we can culture community members and then recreate and easily manipulate communities in the lab,” researchers wrote.