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Revisiting the intrinsic mycobiome in pancreatic cancer

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Matters Arising to this article was published on 02 August 2023

The Original Article was published on 02 October 2019

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Fig. 1: QIIME2 reanalysis of human pancreatic ITS sequencing data made publicly available by Aykut et al.
Fig. 2: QIIME2 reanalysis of human faecal ITS sequencing data made publicly available by Aykut et al.

Data availability

The sequencing dataset generated in the experiments conducted by Aykut et al. is available in the NCBI SRA (https://www.ncbi.nlm.nih.gov/sra; PRJNA557226). Raw count and taxonomy tables generated by QIIME2 and DADA2 as part of our reanalysis of these original sequencing data are available in a public GitHub repository (https://github.com/afletch00/Fungi-Nature-2022).

Code availability

The scripts for the QIIME2 and DADA2 pipelines and downstream analyses performed in R are available in a public GitHub repository (https://github.com/afletch00/Fungi-Nature-2022).

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Acknowledgements

We thank the Duke University School of Medicine for use of the Sequencing and Genomic Technologies Shared Resource, which provided services for sequence analysis; and A. N. Fletcher for providing graphical consultation and colour palette development. This work was funded by the Duke University School of Medicine through a grant from the Duke Microbiome Center. M.S.K. was supported by a National Institutes of Health Career Development Award (K23-AI135090). A.M.E. was supported by a National Institutes of Health T-32 grant (T32-CA093245) for translational research in surgical oncology.

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Authors and Affiliations

  1. Department of Surgery, Division of Surgical Oncology, Duke University School of Medicine, Durham, NC, USA

    Ashley A. Fletcher, Austin M. Eckhoff & Peter J. Allen

  2. Division of Pediatric Infectious Diseases, Associate Director of the Duke Microbiome Center, Duke University, Durham, NC, USA

    Matthew S. Kelly

Authors
  1. Ashley A. Fletcher
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  2. Matthew S. Kelly
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  3. Austin M. Eckhoff
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  4. Peter J. Allen
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Contributions

A.A.F. was primarily responsible for sequencing data analyses, interpretation of findings and preparation of the manuscript. M.S.K. assisted with sequencing data analyses, interpretation of the results and preparation of the manuscript. A.M.E. assisted in data analyses and review of the manuscript. P.J.A. contributed to the interpretation of the study findings, and reviewed and revised the manuscript. All authors reviewed and approved submission of the final manuscript.

Corresponding author

Correspondence to Peter J. Allen.

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The authors declare no competing interests.

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Extended data figures and tables

Extended Data Fig. 1 DADA2 analysis by Fletcher et al. of ITS sequencing data from Aykut et al. human pancreatic tissue samples.

a, Quality plot of raw sequencing reads. The y-axis represents the Phred quality score and the x-axis represents the cycle, which corresponds to the base position of sequencing reads. The mean quality score at each base position is shown by a green line and the quartiles of the quality score distribution are shown by orange lines. The number of sequencing reads in each sample is shown in red font. The red line shows the scaled proportion of reads that extend to at least that position. b, Box plots depicting fungal reads in normal pancreas tissue (n = 5 biologically independent samples) and pancreatic ductal adenocarcinoma (PDAC) tissue (n = 13 biologically independent samples) c, Box plots depicting sequencing reads assigned to the fungal genus Malassezia in normal pancreas (n = 5 biologically independent samples) and PDAC tissue (n = 13 biologically independent samples). d, Relative abundances, and e, read counts of the top ten fungal genera in pancreatic tissue samples from healthy individuals and patients with PDAC. Box plot minima and maxima bounds represent the 25th and 75th percentiles, respectively; the centre bound represents the median. Whiskers extend to 1.5 times the interquartile range (IQR). P values were estimated using two-sided Wilcoxon rank-sum tests (b,c). Individual data points are shown.

Extended Data Fig. 2 DADA2 analysis by Duke Genomic Analysis and Bioinformatics Core of ITS sequencing data from Aykut et al. human pancreatic tissue samples.

a, Box plots depicting fungal reads in normal pancreas tissue (n = 5 biologically independent samples) and pancreatic ductal adenocarcinoma (PDAC) tissue (n = 13 biologically independent samples) b, Box plots depicting sequencing reads assigned to the fungal genus Malassezia in normal pancreas tissue (n = 5 biologically independent samples) and PDAC tissue (n = 13 biologically independent samples). c, Relative abundances, and d, read counts of the top ten fungal genera in pancreatic tissue samples from healthy individuals and patients with PDAC. Box plot minima and maxima bounds represent the 25th and 75th percentiles, respectively; the centre bound represents the median. Whiskers extend to 1.5 times the interquartile range (IQR). P values were estimated using two-sided Wilcoxon rank-sum tests (a,b). Individual data points are shown.

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Fletcher, A.A., Kelly, M.S., Eckhoff, A.M. et al. Revisiting the intrinsic mycobiome in pancreatic cancer. Nature 620, E1–E6 (2023). https://doi.org/10.1038/s41586-023-06292-1

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