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Genomic Study Explores Adaptations Found in Fungi Used for Making Cheese


NEW YORK (GenomeWeb) – Using new and existing Penicillium genomes, a French team has uncovered horizontal gene transfer events that appear to lend some fungal species traits that make them particularly suited for cheese production.

As they reported today in Current Biology, the researchers compared 10 Penicillium genomes, including the P. roqueforti (used to make Roquefort and other blue cheeses) and P. camemberti, which is used for making soft cheeses such as Camembert.

Their results suggest Penicillium domestication for cheese production has hinged on horizontal gene transfer events — from the transfer of genes suspected of aiding in cheese nutrient use to gene swapping that speeds up fungal growth on cheese.

The team speculated that such findings may have implications for improving cheese production, while highlighting the possibility of unintended horizontal gene transfer events that could have food spoilage or safety consequences.

"We were able to identify genes that are directly involved in the adaptation to cheese in Penicillium, opening the way for strain improvement, in particular for obtaining fast-growing strains," co-corresponding author Antoine Branca, an evolution researcher affiliated with the University of Paris-Sud and CNRS, said in a statement.

Nevertheless, the results "raise concerns about food safety," Branca added, "because they suggest that the co-occurrence of different fungal species in the same food product allows genes to be transferred from one species to the other frequently."

Fungi may not be the first organisms that spring to mind for modeling domestication. Even so, the team reasoned that the diverse species and strains employed for producing cheese could offer a peek at adaptations behind fungal selection for this purpose.

The researchers focused on Penicillium fungi, which are found in many different environments.

During independent selection events, they explained, the P. roqueforti and P. camemberti species have been selected for physical features, metabolic traits, and aromatic characteristics desired for making specific cheese types.

After sequencing and assembling draft genomes for five Penicillium representatives, they performed a comparative analysis that brought in existing genome sequence data on several more species.

All told, the team considered 10 Penicillium species, including forms of P. roqueforti, and P. camemberti used in industrial cheese production, along with species implicated as cheese contaminants.

The researchers also included sequences from four Aspergillus species to place in an outgroup in their phylogenetic analysis.

With these data, they uncovered more than 100 horizontal gene transfer events in the Penicillium species.

Seven transfers were especially large, spanning 10,000 bases or more, Branca and colleagues reported, and at least two of the transferred sequences contained genes believed to aid in growth in and on cheese — results verified by follow-up experiments.

In the cheese-associated species, genes within these horizontally transferred sequences, which included genes expressed during cheese maturation, seemed to lend fungi a growth edge on cheese. On the other hand, the team's experiments suggest cheese-associated species are outcompeted by other Penicillium species in minimal growth media.

"It was striking to find such a good match between the putative functions of some genes in the horizontally acquired regions and the function we expected to be essential for metabolizing cheese," co-corresponding author Tatiana Giraud, also with the University of Paris-Sud and CNRS, said in a statement.

Horizontal gene transfer events appeared to be especially common in P. camemberti, a species descended from fungi used to make blue-gray cheeses in the 19th century. A related species called P. biforme, which are a common ancestor of the two species, also showed signs of historically higher-than-usual horizontal gene transfer events in their genomes.

Likewise, the team saw frequent horizontal gene transfer in P. roqueforti, a genetically diverse species that has been associated with wood and silage in addition to its role in cheese production.