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QIIME 2 FMT Book

This tutorial was orignally made for the 2024 ITN / QIIME 2 Workshop, taught 27 - 29 August 2024 at the National Institutes of Health. If you are interested in the original workshop tutorial, please visit: https://q2-cat-book.readthedocs.io/en/2024.08.27-q2-itn/. This tutorial is now the offical documentation for the q2-fmt plugin.

This tutorial will walk you through all the functionality available in q2-fmt. We will start with a metadata file and feature table. We will discuss choosing an even sampling depth and generating diversity metrics so that we are prepared to run our data through q2-fmt. Grab a cup of coffee or tea ☕, and lets jump right in!

The following readings will provide background information for this tutorial. These are presented in priority order.

  1. Assessing Engraftment Following Fecal Microbiota Transplant (Herman et al. (2024))
  2. Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant (Taur et al. (2018))
  3. Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients (Liao et al. (2021))
  4. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 (Bolyen et al. (2019))
  5. q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data (Bokulich et al. (2018))
  6. Getting started with QIIME 2
  7. Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops (Dillon et al. (2021))

Thank you to our funders

This tutorial was funded in part by NIH National Cancer Institute Informatics Technology for Cancer Research grant 1U24CA248454-01 to JGC.

The preparation and dissemination of the data used in this tutorial was funded in part by the National Institutes of Health (NIH) grants U01 AI124275, R01 AI137269 and U54 CA209975 to Joao B. Xavier.

This website is built with MyST Markdown and Jupyter Book, which are supported in part with funding from the Alfred P. Sloan Foundation.

Reusing

q2-fmt-book by Caporaso Lab is licensed under CC BY-NC-SA 4.0.

You are free distribute, remix, adapt, and build upon the material in any medium or format, for noncommercial purposes only, as long as credit is given to the original creator. Adaptations must be shared under the same terms.

References
  1. Herman, C., Barker, B. M., Bartelli, T. F., Chandra, V., Krajmalnik-Brown, R., Jewell, M., Li, L., Liao, C., McAllister, F., Nirmalkar, K., Xavier, J. B., & Gregory Caporaso, J. (2024). Assessing Engraftment Following Fecal Microbiota Transplant. ArXiv, arXiv:2404.07325v1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11042410/
  2. Taur, Y., Coyte, K., Schluter, J., Robilotti, E., Figueroa, C., Gjonbalaj, M., Littmann, E. R., Ling, L., Miller, L., Gyaltshen, Y., Fontana, E., Morjaria, S., Gyurkocza, B., Perales, M.-A., Castro-Malaspina, H., Tamari, R., Ponce, D., Koehne, G., Barker, J., … Xavier, J. B. (2018). Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant. Sci. Transl. Med., 10(460).
  3. Liao, C., Taylor, B. P., Ceccarani, C., Fontana, E., Amoretti, L. A., Wright, R. J., Gomes, A. L. C., Peled, J. U., Perales, M.-A., van den Brink, M. R. M., Littmann, E., Pamer, E. G., Schluter, J., & Xavier, J. B. (2021). Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients. Sci Data, 8(1), 71.
  4. Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., … Caporaso, J. G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(8), 852–857. 10.1038/s41587-019-0209-9
  5. Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodrı́guez, A. M., Chase, J., … Caporaso, J. G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol.
  6. Bokulich, N. A., Dillon, M. R., Zhang, Y., Rideout, J. R., Bolyen, E., Li, H., Albert, P. S., & Caporaso, J. G. (2018). q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data. mSystems, 3(6), e00219-18. 10.1128/mSystems.00219-18
  7. Bokulich, N. A., Dillon, M. R., Zhang, Y., Rideout, J. R., Bolyen, E., Li, H., Albert, P. S., & Caporaso, J. G. (2018). q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data. mSystems, 3(6).
  8. Dillon, M. R., Bolyen, E., Adamov, A., Belk, A., Borsom, E., Burcham, Z., Debelius, J. W., Deel, H., Emmons, A., Estaki, M., Herman, C., Keefe, C. R., Morton, J. T., Oliveira, R. R. M., Sanchez, A., Simard, A., Vázquez-Baeza, Y., Ziemski, M., Miwa, H. E., … Caporaso, J. G. (2021). Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. PLOS Computational Biology, 17(6), e1009056. 10.1371/journal.pcbi.1009056
  9. Dillon, M. R., Bolyen, E., Adamov, A., Belk, A., Borsom, E., Burcham, Z., Debelius, J. W., Deel, H., Emmons, A., Estaki, M., Herman, C., Keefe, C. R., Morton, J. T., Oliveira, R. R. M., Sanchez, A., Simard, A., Vázquez-Baeza, Y., Ziemski, M., Miwa, H. E., … Caporaso, J. G. (2021). Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. PLoS Comput. Biol., 17(6), e1009056.
Tutorial
Assessing engraftment extent with q2-FMT