Supplementary Materials

Supplementary Material for:

Dysbiosis of the Gut Microbiota Is Associated with HIV Disease Progression and Tryptophan Catabolism

Ivan Vujkovic-Cvijin, Richard M. Dunham, Shoko Iwai, Michael C. Maher, Rebecca G. Albright, Mara J. Broadhurst, Ryan D. Hernandez, Michael M. Lederman, Yong Huang, Ma Somsouk, Steven G. Deeks, Peter W. Hunt, Susan V. Lynch,* Joseph M. McCune*

*Corresponding author. E-mail: susan.lynch@ucsf.edu (S.V.L.); mike.mccune@ucsf.edu (J.M.M.)

Published 10 July 2013, Sci. Transl. Med. 5, 193ra91 (2013)
DOI: 10.1126/scitranslmed.3006438

This PDF file includes:

  • Fig. S1. Gross bacterial community metrics do not differ significantly across subject groups or intrasubject samples.
  • Fig. S2. Comparisons of qPCR measurements and PhyloChip relative abundance measurements (MFI) for selected taxa of interest.
  • Fig. S3. Genus and immunologic parameter identities for genera bearing one or more correlation with unadjusted P < 0.005, from analyses including all HIV-infected subjects studied.
  • Fig. S4. PCA characteristics.
  • Fig. S5. HAART causes a shift in DMC composition toward the healthy, uninfected state in two subjects.
  • Fig. S6. Comparison of adjustment variables (antibiotics usage, days on HAART, age) to PC1.
  • Fig. S7. Relationships between IDO1 expression, IDO1 activity, T cell differentiation, and type II interferon.
  • Fig. S8. Bacterial taxa that predict plasma Kyn/Trp ratios in a multivariate machine-learning analysis preferentially encode genetic homologs of tryptophan catabolism enzymes involved in the kynurenine pathway.
  • Fig. S9. Data distribution of RS and P values for all taxa compared to all immunologic variables in Spearman correlation tests.
  • Table S1. Patient cohort data.
  • Legends for tables S2 and S3
  • Table S4. Spearman correlations between PC1 and immunologic variables among all HIV-infected subjects.
  • Table S5. Spearman correlations between PC1 and immunologic variables among HIV+ subjects on HAART.
  • Table S6. Comparisons of PC1 marker of dysbiosis to gut inflammatory gene expression in whole rectosigmoid biopsy specimens.
  • Legend for table S7

[Download PDF]

Other Supplementary Material for this manuscript includes the following:

  • Table S2 (Microsoft Excel format). DMC taxon phylogenetic classifications and statistical analyses.
  • Table S3 (Microsoft Excel format). Spearman correlations between individual taxa of the DMC and markers of disease progression, as calculated among all HIV-infected subjects.
  • Table S7 (Microsoft Excel format). Spearman correlation to Kyn/Trp genus ranks, and analysis of kynurenine pathway metabolic enzymes (those involved in metabolism of tryptophan to 3-HAA) in bacteria.

[Tables S2, S3, and S7]