GuptaA_2019

The study

Gut microbiome of colorectal cancer (CRC) patients in India (Gupta et al. 2019)

30 CRC patients and 30 healthy controls from Bhopal and Kerala
Controls from an earlier study of healthy Indians (Dhakan et al. 2019)
Stool shotgun metagenomes, profiles from curatedMetagenomicData

Import the data

Files and import script: github.com/microbiome/data › GuptaA_2019

library(mia)
library(ape)

url <- "https://raw.githubusercontent.com/microbiome/data/main/GuptaA_2019"
read <- function(f) read.csv(file.path(url, f), row.names = 1)

tse <- TreeSummarizedExperiment(
    assays  = list(counts = as.matrix(read("taxonomy_abundance.csv"))),
    rowData = read("taxonomy_table.csv"),
    colData = read("sample_metadata.csv"),
    rowTree = read.tree(file.path(url, "phylogeny.tree"))
)

The data object

tse

class: TreeSummarizedExperiment 
dim: 308 60 
metadata(0):
assays(1): counts
rownames(308): species-Escherichia_coli species-Alistipes_putredinis
  ... species-Campylobacter_ureolyticus
  species-Prevotella_sp._oral_taxon_376
rowData names(7): superkingdom phylum ... genus species
colnames(60): GupDM_A_11 GupDM_A_15 ... GupDM_JO GupDM_JP
colData names(27): study_name subject_id ... disease_stage
  disease_location
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
rowLinks: a LinkDataFrame (308 rows)
rowTree: 1 phylo tree(s) (10430 leaves)
colLinks: NULL
colTree: NULL

Samples

	Bhopal	Kerala
Control	26	4
CRC	15	15

	Female	Male
Control	18	12
CRC	12	18

Age 22–75 years (median 57); CRC stage, location and TNM available for patients.

Warning

Location and study are partly confounded with disease status: most controls come from Bhopal, and controls and patients come from different studies.

Composition at a glance

Try it

Practise the workflow on this data set:

Agglomeration
Transformation
Alpha diversity and beta diversity: do CRC patients and controls differ?

References

Dhakan, D. B., A. Maji, A. K. Sharma, R. Saxena, J. Pulikkan, T. Grace, A. Gomez, J. Scaria, K. R. Amato, and V. K. Sharma. 2019. “The Unique Composition of Indian Gut Microbiome, Gene Catalogue, and Associated Fecal Metabolome Deciphered Using Multi-Omics Approaches.” GigaScience 8 (3): giz004. https://doi.org/10.1093/gigascience/giz004.

Gupta, Ankit, Darshan B. Dhakan, Abhijit Maji, Rituja Saxena, Vishnu Prasoodanan P. K., Shruti Mahajan, Joby Pulikkan, et al. 2019. “Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India.” mSystems 4 (6): e00438–19. https://doi.org/10.1128/msystems.00438-19.