ArticleThe ISME journal2022
Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures.
Article in The ISME journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 51 citations in OpenAlex.
- Hybrid genome assembly and phenotypic assays reveal carbohydrate metabolism diversity in Lacticaseibacillus strains.Applied microbiology and biotechnology · 2026Article
- Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.Science advances · 2026Article
- Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages.NPJ biofilms and microbiomes · 2026Article
- Innovative Systems Biology in Baijiu Fermentation: Unveiling Omics Landscapes and Microbial Synergy.Foods (Basel, Switzerland) · 2026Review
- Genomic and functional analysis of stress-responsive prophages inFrontiers in microbiology · 2026Article
- Role of microbial interactions in the impaired cultivability of thermophilic lactic acid bacteria in natural whey starter for Parmigiano Reggiano PDO cheese production.Frontiers in microbiology · 2026Article
- Exploring sub-species variation in food microbiomes: a roadmap to reveal hidden diversity and functional potential.Applied and environmental microbiology · 2025Review
- Lactococcal phage-host profiling through binding studies between cell wall polysaccharide types andMicrobial genomics · 2025Article
- Comparative genome analysis of 15 Streptococcus thermophilus strains isolated from Turkish traditional yogurt.Antonie van Leeuwenhoek · 2025Article
- Analytical Mapping of Swiss Hard Cheese to Highlight the Distribution of Volatile Compounds, Aroma, and Microbiota.Journal of agricultural and food chemistry · 2025Article
- Unraveling the multiple interactions between phages, microbes and flavor in the fermentation of strong-flavor Baijiu.Bioresources and bioprocessing · 2025Article
- Microbiota of Cheese Ecosystems: A Perspective on Cheesemaking.Foods (Basel, Switzerland) · 2025Review
- Genomic diversity and functional adaptation ofFrontiers in microbiology · 2025Article
- Long-read metagenomics gives a more accurate insight into the microbiota of long-ripened gouda cheeses.Frontiers in microbiology · 2025Article
- Genomic and phenotypic imprints of microbial domestication on cheese starter cultures.Nature communications · 2024Article
- Serial fermentation in milk generates functionally diverse community lineages with different degrees of structure stabilization.mSystems · 2024Article
- Article
- A multifaceted investigation of lactococcal strain diversity in undefined mesophilic starter cultures.Applied and environmental microbiology · 2024Article
- Metabolic profiles outperform the microbiota in assessing the response of vaginal microenvironments to the changed state of HPV infection.NPJ biofilms and microbiomes · 2024Article
- Genetic diversity and phylogenetic relationships of Streptococcus thermophilus isolates from traditional Turkish yogurt: multilocus sequence typing (MLST).Archives of microbiology · 2024Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.