Supplementary Materials

Supplementary Material for:

The effects of micronutrient deficiencies on bacterial species from the human gut microbiota

Matthew C. Hibberd, Meng Wu, Dmitry A. Rodionov, Xiaoqing Li, Jiye Cheng, Nicholas W. Griffin, Michael J. Barratt, Richard J. Giannone, Robert L. Hettich, Andrei L. Osterman, Jeffrey I. Gordon*

*Corresponding author. Email: jgordon{at}wustl.edu

Published 17 May 2017, Sci. Transl. Med. 9, eaal4069 (2017)
DOI: 10.1126/scitranslmed.aal4069

This PDF file includes:

  • Fig. S1. Comparisons of community structure across experimental stages.
  • Fig. S2. Relative abundances of B. vulgatus ATCC 8482 and B. dorei DSM 17855 in gnotobiotic mice across experimental stages and treatment groups.
  • Fig. S3. Characterization of the B. vulgatus ATCC 8482 INSeq library.
  • Fig. S4. Maximum likelihood phylogenetic tree of BVU0240/AcrR orthologs identified in human gut–associated Bacteroides and other members of the family Bacteroidaceae.
  • Fig. S5. DNA binding characteristics of AcrRBV and AcrRBD in the presence and absence of possible effectors.

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Nutritional characteristics of experimental micronutrient-deficient and micronutrient-sufficient diets.
  • Table S2 (Microsoft Excel format). Ninety-two sequenced, human gut–derived bacterial strains.
  • Table S3 (Microsoft Excel format). COPRO-Seq analysis of community composition in fecal samples.
  • Table S4 (Microsoft Excel format). Influence of micronutrient deficiencies on the relative abundances of specific taxa.
  • Table S5 (Microsoft Excel format). Identification of community members that exhibit significant changes in their abundance as a function of diet treatment and/or time.
  • Table S6 (Microsoft Excel format). Microbial RNA-seq analysis of changes in community metatranscriptome as a function of diet treatment with grouping of transcripts into KO groups.
  • Table S7 (Microsoft Excel format). Microbial RNA-seq analysis of changes in B. vulgatus gene expression as a function of diet treatment with grouping of transcripts into KO groups.
  • Table S8 (Microsoft Excel format). Strain-level microbial RNA-seq analysis of the effects of vitamin A on gene expression (summarized at the level of KO groups).
  • Table S9 (Microsoft Excel format). Mouse weights as a function of diet treatment and time.
  • Table S10 (Microsoft Excel format). In vitro retinoid sensitivities of Bacteroides strains.
  • Table S11 (Microsoft Excel format). Strains, primers, and plasmids used in this study.
  • Table S12 (Microsoft Excel format). Microbial RNA-seq analysis of differential gene expression between wild-type B. vulgatus and Tn mutants (DESeq2).
  • Table S13 (Microsoft Excel format). Bioinformatic characterization of AcrR regulons in human gut Bacteroides strains.
  • Table S14 (Microsoft Excel format). High-resolution quantitative MS-based proteomic analysis of wild-type B. vulgatus cultured in the presence of 1 μM retinol versus vehicle alone (0.02% DMSO).
  • Table S15 (Microsoft Excel format). Effects of retinol, bile acids, and PAβN on growth of wild-type and mutant strains of B. vulgatus and wild-type B. dorei.
  • Table S16 (Microsoft Excel format). UPLC-MS analysis of the effects of dietary micronutrient deficiency on fecal bile acid metabolites.

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