A network of cheese rind microorganisms?

Cheese making is about 8,000 years old, and there are now about 1,000 distinct types of cheese throughout the world. As with most ancient crafts, the art of making cheese is to get the microbes to do most of the work for you.

To this end, there has been much interest in the microbial communities that occur in cheese rinds (the bit around the outside). Different communities are expected to be associated with different styles of cheese, since the production process can be quite different. This is shown in the first figure, which emphasizes that much of the difference between cheeses is due to different maturation procedures.

From Wolfe et al. (2014).

Recently, Wolfe BE, Button JE, Santarelli M, and Dutton R (2014. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 158: 422-433) had a look at the dominant genera of bacteria and microfungi in the rind communities of 137 different types of cheese. They don't actually tell us much about which cheeses these were, merely claiming:

We attempted to evenly sample across rind type (24 bloomy rind cheeses, 52 washed rind cheeses, and 61 natural rind cheeses) and geographic regions (87 European cheeses across 9 countries; 50 American cheeses across 13 states from the West Coast to the east Coast). We also attempted to sample across different milk types (77 cow milk, 34 goat milk, 21 sheep milk, and 5 mixed milk) and milk treatments (99 raw milk, 38 pasteurized).

Based on sequencing the bacterial 16S and fungal ITS loci, the authors identified 14 bacterial and 10 fungal genera (moulds and yeasts) that occurred with an average abundance of >1%, as shown in the next figure.

The 137 rind samples with their bacterial (middle row) and fungal (bottom row) genera indicated
by different colours. The order of the samples was determined by UPGMA clustering (top row).

The authors also used shotgun metagenomic sequencing to identify a range of genes in the microorganisms. They present a phylogeny of one particular gene (shown in the next figure) that shows a close relationship between some of the cheese microbes and marine bacteria:

The widespread distribution and high abundance of marine-associated gamma-Proteobacteria, enriched in both washed and bloomy rind cheeses, was an unexpected finding in our survey of taxonomic diversity ... One possible source of these marine microbes is the sea salt used in cheese production.

[Note: the other cheese rind bacterium shown in the phylogeny, Brevibacterium linens, is the one responsible for the unbelievable smell of washed-rind cheeses such as Epoisses, Münster and Limburger. It is also responsible for personal-hygiene issues such as foot odour. You can imagine how it first got into cheese making!]

However, Ropars J, Cruaud C, Lacoste S, and Dupont J (2012. A taxonomic and ecological overview of cheese fungi. International Journal of Food Microbiology 155: 199-210), in a related study, have pointed out the usual problem with microbial phylogenies: gene trees are frequently incongruent. So, the gene phylogeny shown above is not likely to be the species phylogeny. It would thus be of great interest to investigate the full microbial network, rather than looking at a single tree.