NOTE While we continue to maintain this R package, the development has been discontinued as we have shifted to supporting methods development based on the new TreeSummarizedExperiment data container, which provides added capabilities for multi-omics data analysis. Check the miaverse project for details.

Tools for the exploration and analysis of microbiome profiling data sets.

This R package extends the phyloseq data container. The package is actively maintened but we have discontinued the development and shifted to support methods development based on the (Tree)SummarizedExperiment data containers, see microbiome.github.io for more details.

See the package tutorial.

Kindly cite as follows: "Leo Lahti, Sudarshan Shetty et al. (Bioconductor, 2017). Tools for microbiome analysis in R. Microbiome package version 1.23.1. URL: http://microbiome.github.com/microbiome. See also the relevant references listed in the manual page of each function.

Contributions and feedback are very welcome:

• Issue Tracker
• Pull requests
• Subscribe to the mailing list ([email protected])
• Gitter chat room
• Star us on the Github page

Below some publications that utilize the tools implemented in this package. The list of publications is not exhaustive. Let us know if you know of further publications using the microbiome package; we are collecting these on the website.

Intestinal microbiome landscaping: Insight in community assemblage and implications for microbial modulation strategies. Shetty S, Hugenholtz F, Lahti L, Smidt H, de Vos WM, Danchin A. FEMS Microbiology Reviews fuw045, 2017.

Metagenomics meets time series analysis: unraveling microbial community dynamics Faust K, Lahti L, Gonze D, de Vos WM, Raes J. Current Opinion in Microbiology 15:56-66 2015.

Tipping elements in the human intestinal ecosystem Lahti L, Salojärvi J, Salonen A, Scheffer M, de Vos WM. Nature Communications 5:4344, 2014.

Fat, Fiber and Cancer Risk in African, Americans and Rural Africans O’Keefe S, Li JV, Lahti L, Ou J, Carbonero F, Mohammed K, Posma JM, Kinross J, Wahl E, Ruder E, Vipperla K, Naidoo V, Mtshali L, Tims S, Puylaert PGB, DeLany J, Krasinskas A, Benefiel AC, Kaseb HO, Newton K, Nicholson JK, de Vos WM, Gaskins HR, Zoetendal EG. Nature Communications 6:6342, 2015.

Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data Lahti L, Salonen A, Kekkonen RA, Salojärvi J, Jalanka-Tuovinen J, Palva A, Orešič M, de Vos WM. PeerJ 1:e32, 2013.

The adult intestinal core microbiota is determined by analysis depth and health status Salonen A, Salojärvi J, Lahti L, and de Vos WM. Clinical Microbiology and Infection 18(S4):16 20, 2012.

Main developer: Leo Lahti

Main co-authors: Sudarshan Shetty

Contributors

Thanks for [@johanneskoester] and [@nick-youngblut] for contributing Bioconda installation recipe.

The work has been supported by the following bodies:

• Academy of Finland (grants 256950, 295741, 307127)
• University of Turku, Department of Mathematics and Statistics
• Molecular Ecology group, Laboratory of Microbiology, Wageningen University, Netherlands

This work extends the independent phyloseq package and data structures for R-based microbiome analysis.