Fuchsmann, P. | bioRxiv Science

bioRxiv2023

Scoary2: Rapid association of phenotypic multi-omics data with microbial pan-genomes

Genomic screening of bacteria is common practice to select strains with desired properties. However, 40-60% of all bacterial genes are still unknown, making capturing the phenotype an important part of the selection process. While omics-technologies collect high-dimensional phenotypic data, it remains challenging to link this information to genomic data to elucidate the impact of specific genes on phenotype. To this end, we present Scoary2, an ultra-fast software for microbial genome-wide association studies (mGWAS), enabling integrative data exploration. As proof of concept, we explore the metabolome of 44 yogurts with different strains of Propionibacterium freudenreichii, discovering two genes affecting carnitine metabolism.

bioinformatics↗

bioRxiv2021

Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures

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.

microbiology↗