Multilayer analysis reveals extensive hidden population complexity in a dairy starter microbiome comprising few species

The intricate makeup of microbiomes with minimal species diversity remains a largely unexplored area of study. Researchers combined 111 unique isolate genomes with advanced long-read metagenomic data to examine an unidentified mesophilic dairy starter. This analysis uncovered that closely related strains possessed unique combinations of traits relevant to fermentation processes and protection against viral infections, which included distinct surface polysaccharide types, plasmids, prophages, protective mechanisms, and DNA methylation patterns.

Metagenomics data exposed supplementary components and inferred relationships with host organisms. Nonetheless, the degree of overlap between the two analytical techniques utilized for core-genome lineages and additional microbial repertoires was insufficient, revealing complementary yet incomplete discoveries. The investigation found that the most prevalent cell wall polysaccharide (accounting for 29.6% of the population) was not detected in any of the isolated strains.

Methylation signatures derived from the metagenomic data corroborated the assignment of 36 species-level plasmid-host relationships, with this finding confirmed in nine out of ten testable instances. The study uncovered a significant level of combinatorial diversity that remained undetected by either method individually, providing a potential molecular explanation for phage resistance. This level of diversity likely represents just a fraction of the true population complexity.