Obtain the Lahti Microbiome and Lipid data

Obtain the microbiome and lipid data from Lahti et al. (2013).

LahtiMLData()

LahtiMData()

peerj32()

Value

for LahtiMLData a MultiAssayExperiment object with TreeSummarizedExperiment and a SummarizedExperiment, for LahtiMData a TreeSummarizedExperiment

Details

The LahtiML dataset contains high-throughput profiling data from 389 human blood serum lipids and 130 intestinal genus-level bacteria from 44 samples (22 subjects from 2 time points; before and after probiotic/placebo intervention). The data set can be used to investigate associations between intestinal bacteria and host lipid metabolism

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 time points, sex, subject identifier, sample identifier and treatment group.

Row metadata of the microbiome data 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. (2013): Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data. PeerJ 1:e32 https://doi.org/10.7717/peerj.32

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

mae <- LahtiMLData()
#> 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
#> see ?microbiomeDataSets and browseVignettes('microbiomeDataSets') for documentation
#> loading from cache
tse <- LahtiMData()
#> 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