Deconstructing and Reconstructing Cheese Rind Microbiomes for Experiments in Microbial Ecology and Evolution

AbstractCheese rind microbiomes are useful model systems for identifying the mechanisms that control microbiome diversity. Here, we describe the methods we have optimized to first deconstruct in situ cheese rind microbiome diversity and then reconstruct that diversity in laboratory environments to conduct controlled microbiome manipulations. Most cheese rind microbial species, including bacteria, yeasts, and filamentous fungi, can be easily cultured using standard lab media. Colony morphologies of taxa are diverse and can often be used to distinguish taxa at the phylum and sometimes even genus level. Through the use of cheese curd agar medium, thousands of unique community combinations or microbial interactions can be assessed. Transcriptomic experiments and transposon mutagenesis screens can pinpoint mechanisms of interactions between microbial species. Our general approach of creating a tractable synthetic microbial community from cheese can be easily applied to other fermented foods to develop other model microbiomes. © 2019 by John Wiley & Sons, Inc.Basic Protocol 1: Isolation of cheese rind microbial communitiesSupport Protocol 1: Preparation of plate count agar with milk and saltBasic Protocol 2: Identification of cheese rind bacterial and fungal isolates using 16S and ITS sequencesBasic Protocol 3: Preparation of experimental glycerol stocks of yeasts and bacteriaBasic Protocol 4: Preparation of experimental glycerol stocks of filamentous fungiBasic Protocol 5: Reconstruction of cheese rind microbial communities in vitroSupport Protocol 2: Preparation of lyophilized and powdered cheese curdSupport Protocol 3: Preparation of 10% cheese curd agar plates and tubesBasic Protocol 6: Interaction screens using responding lawnsSupport Protocol 4: Preparation of liquid 2% cheese curdBasic Protocol 7: Experimental evolutionBasic Protocol 8: Measuring community function: pH/acidificationBasic Protocol 9: Measuring community function: Pigment productionBasic Protocol 10: RNA sequencing of cheese rind biofilms