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dysbiosisR

The dysbiosisR package is a collection of functions to calculate six dysbiosis measures from microbiota profiling data. The package currently supports microbiome data organized as phyloseq objects.

Installation

You can install the development version of dysbiosisR like this:

    devtools::install_github("microsud/dysbiosisR")

Load package 

    library(dysbiosisR)

We welcome feedback and suggestions.

How to use

Check out the dysbiosisR vignette and documentation of functions for more details.

Contribute

Contributions and feedback are very welcome:

Cite

Shetty SA, WAA de Steenhuijsen Piters., et al., 2022. dysbiosisR: an R package for calculating microbiome dysbiosis measures.

References

  1. Santiago M, et al., 2019. Microbiome predictors of dysbiosis and VRE decolonization in patients with recurrent C. difficile infections in a multi-center retrospective study. AIMS Microbiol 5:1–18. 10.3934/microbiol.2019.1.1.

  2. Lloyd-Price J, Arze C, Ananthakrishnan AN, et al., 2019. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569:655–662. 10.1038/s41586-019-1237-9.

  3. AlShawaqfeh MK, et al., 2017. A dysbiosis index to assess microbial changes in fecal samples of dogs with chronic inflammatory enteropathy. FEMS Microbiol Ecol 93:1–8. 10.1093/femsec/fix136.

  4. Montassier E, Al-Ghalith GA, Hillmann B, Viskocil K, Kabage AJ, McKinlay CE, Sadowsky MJ, Khoruts A, Knights D. 2018. CLOUD: a non-parametric detection test for microbiome outliers. Microbiome 6:137. 10.1186/s40168-018-0514-4.

  5. Saffouri GB, Shields-Cutler RR, Chen J, Yang Y, Lekatz HR, Hale VL, Cho JM, Battaglioli EJ, Bhattarai Y, Thompson KJ, Kalari KK, Behera G, Berry JC, Peters SA, Patel R, Schuetz AN, Faith JJ, Camilleri M, Sonnenburg JL, Farrugia G, Swann JR, Grover M, Knights D, Kashyap PC. 2019. Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders. Nat Commun 10:2012. 10.1038/s41467-019-09964-7.

  6. Wei, S, Bahl, MI, Baunwall, SMD, Hvas, CL and Licht, TR. 2021. Determining gut microbial dysbiosis: a review of applied indexes for assessment of intestinal microbiota imbalances. Applied and Environmental Microbiology, 87(11), pp.e00395-21.

  7. Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D’Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE, Dunklebarger MF, Knight R, Jansson JK. 2017. Dynamics of the human gut microbiome in inflammatory bowel disease. Nat Microbiol 2:17004. 10.1038/nmicrobiol.2017.4.

Acknowledgement

This work was done at the Department of Medical Microbiology and Infection Prevention at UMC Groningen in collaboration with the Microbiome Group at the RIVM.

Contact

Sudarshan A. Shetty (sudarshanshetty9[@]gmail[dot]com)
Susana Fuentes (susana[dot]fuentes[@]rivm[dot]nl)