Supplementary Material

Supplementary Material for:

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

Peter J. Turnbaugh, Vanessa K. Ridaura, Jeremiah J. Faith, Federico E. Rey, Rob Knight, Jeffrey I. Gordon*

*To whom correspondence should be addressed. E-mail: jgordon{at}wustl.edu

Published 11 November 2009, Sci. Transl. Med. 1, 6ra14 (2009)
DOI: 10.1126/scitranslmed.3000322

This PDF file includes:

  • Materials and Methods
  • References
  • Fig. S1. Phylogeny of the Erysipelotrichi.
  • Fig. S2. Rarefaction analysis of the gut microbiota of humanized mice.
  • Fig. S3. Unweighted UniFrac-based clustering of V2 16S rRNA gene surveys.
  • Fig. S4. Assembly of the human gut microbiota in suckling, weaning, and young adult C57BL/6J mice.
  • Fig. S5. Analysis of the in vivo Erysipelotrichi population, anchored to the C. innocuum SB23 draft genome.
  • Table S1–16 legends. [See below for instructions on downloading tables.]

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Other Supplementary Material for this manuscript includes the following:
(available at www.sciencetranslationalmedicine.org/cgi/content/full/1/6/6ra14/DC1)

Tables S1 – S16. (In Microsoft Excel format).

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3000322_tables_s1_s16.zip (222 KB)

  • Table S1. V2 16S rRNA gene sequencing statistics from human donor and two generations of recipient humanized mice.
  • Table S2. Full-length 16S rRNA gene sequencing statistics.
  • Table S3. Abundance of class-level bacterial taxa in the gut microbiota.
  • Table S4. Abundance of genus-level bacterial taxa in the gut microbiota.
  • Table S5. V2 16S rRNA gene sequencing statistics from transplantation of a frozen human fecal sample.
  • Table S6. V2 16S rRNA gene sequencing statistics from the assembly of the humanized mouse gut microbiota.
  • Table S7. V2 16S rRNA gene sequencing statistics from humanized mouse biogeography analysis.
  • Table S8. Microbiome sequencing statistics (fecal samples).
  • Table S9. Genomes in the human gut microbe database.
  • Table S10. Relative abundance of KEGG orthologous groups (KOs) in Western diet–associated pathways (% of KO assignments).
  • Table S11. C. innocuum strain SB23 genome sequencing statistics.
  • Table S12. Number of genes assigned to glycoside hydrolase family 1 in gut Firmicutes and Bacteroidetes.
  • Table S13. cDNA sequencing statistics.
  • Table S14. C. innocuum strain SB23 genes up-regulated in the ceca of humanized mice fed the Western diet relative to the LF/PP diet.
  • Table S15. Primers used for qRT-PCR analysis.
  • Table S16. Community gene clusters differentially expressed in the ceca of humanized mice fed the Western diet relative to the LF/PP diet.

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