Obtain the Lahti Western Adult microbiome data

Obtain the microbiome data from Lahti et al. (2014).

LahtiWAData()

atlas1006()

Value

a TreeSummarizedExperiment

Details

The LahtiWA dataset contains high-throughput genus-level microbiota profiling with HITChip for 1006 western adults with no reported health complications, reported in Lahti et al. (2014).

This data set is based on the Human Intestinal Tract (HIT)Chip phylogenetic 16S microarray (Rajilic-Stojanovic et al. 2009. This profiling technology differs from the more widely used 16S rRNA amplicon sequencing.

Column metadata includes the age, sex, nationality, DNA extraction method, project identifier, precomputed diversity measurement, BMI group, subject identifier, time information and sample identifier.

Row metadata contains taxonomic information on the Phylum, Family and Genus level.

All data are downloaded from ExperimentHub and cached for local re-use.

References

Lahti L et al. (2014): Tipping elements in the human intestinal ecosystem. Nature Communications 5:4344 (2014) https://doi.org/10.1038/ncomms5344

Rajilic-Stojanovic M, Heilig HG, Molenaar D, Kajander K, Surakka A, Smidt H, de Vos WM (2009). Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol. 11(7):1736-51 https://doi.org/10.1111/j.1462-2920.2009.01900.x

Author

Felix G.M. Ernst and Leo Lahti

Examples

tse <- LahtiWAData()
#> snapshotDate(): 2022-07-22
#> see ?microbiomeDataSets and browseVignettes('microbiomeDataSets') for documentation
#> loading from cache
#> see ?microbiomeDataSets and browseVignettes('microbiomeDataSets') for documentation
#> loading from cache
#> see ?microbiomeDataSets and browseVignettes('microbiomeDataSets') for documentation
#> loading from cache