README.md

Here we provide files associated with our paper:

1. Jupyter notebook containing the bioinformatics pipeline used to process sequencing data* (oral-microbiota-hsct_script.ipynb)
2. Several R scripts used for plotting and statistics (R scripts dir)
3. QIIME 2 artifacts necessary to rerun the analyses (qza dir)
4. Metadata and clinical data (data dir):
   • Mapping file
   • Clinical data
   • ATB usage data
   • Blood cell count data
   • List of blooming events
   • ATB usage variables/classes
   • Microbiota variables/classes

*Raw sequencing data have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB53914. Some samples (analyzed in previous studies) were deposited previously in ENA at EMBL-EBI under accession numbers: PRJEB42862, PRJEB49175. Overall, out of the 444 sequenced samples analyzed in this study, PRJEB53914 contains 315, PRJEB42862 contains 90, and PRJEB49175 contains 39 samples. Refer to the mapping file to associate the universal sample IDs with the metadata used in this study.

If you use this data in a publication, please cite as:

Heidrich, V., et al. (2023) Longitudinal analysis at three oral sites links oral microbiota to clinical outcomes in allogeneic hematopoietic stem-cell transplant. mSpectrum DOI: 10.1128/spectrum.02910-23.