Human exposure to the airbone fungal pathogens Pneumocystis

Cissé OH, Ma L, Jiang C, Snyder M, Kovacs JA. 2020. Humans are selectively exposed to Pneumocystis jirovecii. mBio 11:e03138-19. https://doi.org/10.1128/mBio.03138-19.

Directory:

* src/data/:  workhorse scripts
* src/tools/: utils 
* src/visualization/: R scripts
* data/raw/: SRA ids
* data/raw/summary_v2.csv:  metadata 
* data/processed/Cell_2018/variants:  SNP data
* data/processed/filtered_ctgs: filtered contigs
* data/processed/raw_fig: raw plots

Primary air metagenome sequencing data source:

• Jiang C., et al. Cell. 2018 Sep 20;175(1):277-291.e31. doi: 10.1016/j.cell.2018.08.060.
• Afshinnekoo E., et al. Cell Syst. 2015 Jul 29;1(1):72-87.
• King P, et al. PLoS One 11:e0160124

Pneumocystis genomes

• Pneumocystis jirovecii strain SE8

  • Cisse OH, Pagni M, Hauser PM. 2012. MBio 4:e00428-12.
  • GenBank assembly accession: GCA_000333975.2

• Pneumocystis jirovecii strain RU7

  • Ma L, et al. 2016. Nat Commun 7:10740.
  • GenBank assembly accession: GCA_001477535.1

• Pneumocystis jirovecii strain SE2178

  • Schmid-Siegert E, et al. 2017. MBio 8.
  • GenBank assembly accession: GCA_002571455.1

• Pneumocystis carinii strain B80

  • Ma L, et al. 2016. Nat Commun 7:10740.
  • GenBank assembly accession: GCA_001477545.1

• Pneumocystis carinii strain Ccin

  • Slaven BE, et al.2006. J Eukaryot Microbiol 53 Suppl 1:S89-91.
  • http://pgp.cchmc.org

• Pneumocystis carinii strain SE6

  • Cisse OH, Pagni M, Hauser PM. 2012. MBio 4:e00428-12.

• Pneumocystis murina strain B123

  • Ma L, et al. 2016. Nat Commun 7:10740
  • GenBank assembly accession: GCA_000349005.2