Microbial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemaking
Journal article, 2026
The history of cheesemaking is deeply intertwined with the evolution of microbial communities, from spontaneous fermentation to modern, standardized practices. The rapid technological changes of the last century likely induced profound alterations in cheese microbial communities, yet this remains largely underexplored. Using shotgun metagenomics and 16S rRNA amplicon sequencing, we examined microbial community changes in Raclette du Valais, a traditional Swiss cheese, using preserved wheels from 1875 to 2017 from the same Alpine dairy. Our results reveal that significant differences in microbial community composition coincide with changes in production practices. The oldest cheese harbored a distinct bacterial community, dominated by Lactiplantibacillus paraplantarum , Streptococcus thermophilus , Pseudolactococcus laudensis , and gut-associated taxa. Antibiotic-resistance genes mirrored historical antibiotic use, lactic acid bacteria domestication predated the studied period, and bacteriophage genera from 1875 were already comparable to those of modern cheese factories. These findings highlight how human practices have shaped cheese microbiomes over time.
microbial communities
antibiotic resistance genes
shotgun metagenomics
bacteriophage diversity
lactic acid bacteria
cheesemaking history
16S rRNA amplicon sequencing
historical cheese wheels
Author
Vincent Somerville
Swiss Federal Institute of Technology in Zürich (ETH)
Universite Laval
Marco Meola
DATABIOMIX GmbH
Agroscope
Abigail Nunes-Richards
University of Zürich
Johan Bengtsson Palme
CARe
Chalmers, Life Sciences, Systems and Synthetic Biology
University of Gothenburg
Judith Neukamm
University of Zürich
Kerttu Majander
University of Basel
Marta Pla-Díaz
University of Basel
Meral Turgay
Agroscope
Sylvain Moineau
Universite Laval
Monika Haueter
Agroscope
Hélène Berthoud
Agroscope
Ueli von Ah
Agroscope
Petra Lüdin
Agroscope
Verena J. Schuenemann
University of Zürich
University of Basel
Noam Shani
Agroscope
Current Biology
0960-9822 (ISSN)
Vol. 36 19 4870-4882.e4EMBARK: Establishing a Monitoring Baseline for Antibiotic Resistance in Key environments
Swedish Research Council (VR) (2019-00299), 2022-05-01 -- 2023-12-31.
Surveillance for Emerging Antimicrobial Resistance through Characterization of the uncharted Environmental Resistome
Swedish Research Council (VR) (2023-01721), 2023-12-01 -- 2026-11-30.
Predicting future pathogenicity and antibiotic resistance
Swedish Foundation for Strategic Research (SSF) (FFL21-0174), 2022-08-01 -- 2027-12-31.
Subject Categories (SSIF 2025)
Food Science
Microbiology
DOI
10.1016/j.cub.2026.08.023
PubMed
42785314