Two year monitoring of environmental microbiota and mycobiota of tree fruit packing houses and their effect on the occurrence of L. monocytogenes

Rolon, M.L., Tan, X., Chung, T., Gonzalez-Escalona, N., Chen, Y., Macarisin, D., LaBorde, L.F., Kovac,J. 2023. The composition of environmental microbiota in three tree fruit packing facilities changed over seasons and contained taxa indicative of L. monocytogenes contamination. Microbiome 11, 128.

https://doi.org/10.1186/s40168-023-01544-8

Data analysis workflow:

1. Lm occurrence analysis

2. Compositional data analysis of microbiota and mycobiota

3. Differential abundance analysis by facility and Lm presence

4. Random forest analysis to determine ASVs that classify into Lm positive or negative

5. Core microbiota and network analyses

6. Analysis of Nanopore sequence data

Input files

1. Metadata for 16s
2. Metadata for ITS