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microbiome R package

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Tools for the exploration and analysis of microbiome profiling data sets, in particular large-scale population studies and 16S taxonomic profiling.

Installation and use

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 1.1.10013. 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:

Publications using the microbiome package

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

Co-authors: Sudarshan Shetty


The work has been supported by the following bodies:

This work relies on the independent phyloseq package and data structures for R-based microbiome analysis developed by Paul McMurdie and Susan Holmes.