Microbiome Data Analysis using R Packages

Statistical analysis and graph processing were conducted on R (Version 4.2.3) using RStudio software (Version 2022.07.0). Several packages were used in the analysis: phyloseq (Version 1.42.0) to facilitate the import, storage, handling and analysis of the microbiome data (McMurdie and Holmes, 2013 (link)), as well as to determine alpha diversity. For the latter, both Chao1 and Shannon indexes were calculated. Vegan (Version 2.6-4) package was used for the permutational multivariate analysis of variance (PERMANOVA) using the Bray Curtis metric distance. The mixOmics package was used for sparse partial least squares discriminant analysis (Rohart et al., 2017 (link)) and the microbiomeMarker (Version 1.4) package for the Linear Discriminant Analysis (LDA) effect size (SE). The ggplot2 (Version 3.4.4) package was used for graphical representation of the data.

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Iorizzo M., Bagnoli D., Vergalito F., Testa B., Tremonte P., Succi M., Pannella G., Letizia F., Albanese G., Lombardi S.J, & Coppola R. (2024). Diversity of fungal communities on Cabernet and Aglianico grapes from vineyards located in Southern Italy. Frontiers in Microbiology, 15, 1399968.

Publication 2024

RStudio software

Corresponding Organization :

Other organizations : University of Molise, Università Campus Bio-Medico

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

Alpha diversity (Chao1 and Shannon indexes)
Microbial community composition (assessed using PERMANOVA with Bray Curtis metric distance)
Features that discriminate between groups (identified using sparse partial least squares discriminant analysis and Linear Discriminant Analysis effect size)

control variables

None explicitly mentioned

controls

No positive or negative controls were mentioned in the protocol.

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