UC San Diego

Many aged cheeses consistently develop a bloom of microbes at their surface, called a rind. Proper development of the rind and the underlying cheese’s defining characteristics depends on the specific assembly of a community of microbes at the rind. Oftentimes, the assembly process of rind microbiomes as well as other relevant microbiomes is quite dynamic and results in a series of different dominant community members, called a pattern of ecological succession. The specific factors that shape a specific pattern of succession are only superficially understood. While microbial communities serve as useful study models because of their rapid development in comparison to, for example, a forest, the drivers of their successional patterns are primarily studied observationally or theoretically using sequencing datasets. This dissertation explores the drivers underlying the pattern of succession that occurs during the aging of a natural rind cheese, through both metagenomic investigations of rind microbiome development as well as in vitro experimentation using a model community assembled from the cave-aged rind. We first find that the overarching pattern of succession is driven primarily by two fungal species who modulate the pH of the environment or inhibit population size. I further explore the mechanisms underlying these activities and identify potentially novel mechanisms involved in both stimulation and inhibition of community neighbors. We also show how segregated spatial organization of the rind biofilm may explain why the effects of fungal species are stronger than those of bacteria. And finally, we start to consider how bacteriophage might contribute to rind assembly dynamics, by contributing genetic functions or by generating dynamic patterns at the strain level. I conclude these studies with advice on how our findings can be followed up to further explore and identify mechanisms involved in community assembly both of a cheese rind and potentially of other medicinally-, environmentally-, and industrially-relevant microbiomes.