A brief introduction to HintikkaXOData

Study design

HintikkaXOData is a MultiAssayExperiment containing microbiome, metabolome and biomarker data from a study on the effects of diet and prebiotics on fatty-liver disease in rats (Hintikka et al. 2021).

ExperimentList class object of length 3:
 [1] microbiota: TreeSummarizedExperiment with 12706 rows and 40 columns
 [2] metabolites: TreeSummarizedExperiment with 38 rows and 40 columns
 [3] biomarkers: TreeSummarizedExperiment with 39 rows and 40 columns

The rat population (N = 40) was divided into 4 groups (n = 10), which underwent different diets over a period of 12 weeks. The 4 groups included:

  • high-fat diet without prebiotics

  • high-fat diet with prebiotics

  • low-fat diet without prebiotics

  • low-fat diet with prebiotics

XOS+ XOS-
Low Fat 10 10
High Fat 10 10

XOS: xylooligosaccharide

Microbiota

Microbiome data was obtained by 16S rRNA gene sequencing of bacterial DNA sampled from the cecum of terminated rats. Then, sequence reads were assembled into Operational Taxonomic Units (OTUs).

Relative Abundance (%)
Bacteroidetes 51.3
Firmicutes 39.5
Verrucomicrobia 3.8
Cyanobacteria 2.6
Proteobacteria 2.2

Figure 1: ?(caption)

Metabolites

Metabolome data was obtained from the same cecal samples by nuclear magnetic resonance (NMR) spectroscopy. There is a total of 38 features, corresponding to the different metabolites.

Biomarkers

Biomarkers data were obtained by Western blot from protein homogenates of rat tissues. There is a total of 39 features, corresponding to the biomarkers/site combinations.

Biomarker Function
CS citrate synthase
AST aspartate aminotransferase
ALT alanine aminotransferase
ERK extracellular signal-regulated kinase
IRS1 insulin receptor substrate 1
AKT protein kinase B
IL1b interleukin 1 beta
HAD 3-hydroxyacyl-CoA dehydrogenase 8
CD45 protein tyrosine phosphatase
Name Site
epi epididymal adipose tissue
SCfat mesenteric adopose tissue
mese subcutaneous adipose tissue
liver liver
gastro gastrocnemius muscle
serum serum

References

Hintikka, Jukka, Sanna Lensu, Elina Mäkinen, Sira Karvinen, Marjaana Honkanen, Jere Lindén, Tim Garrels, Satu Pekkala, and Leo Lahti. 2021. “Xylo-Oligosaccharides in Prevention of Hepatic Steatosis and Adipose Tissue Inflammation: Associating Taxonomic and Metabolomic Patterns in Fecal Microbiomes with Biclustering.” International Journal of Environmental Research and Public Health 18 (8): 4049. https://doi.org/10.3390/ijerph18084049.