Additional file 2 of Diet, obesity, and the gut microbiome as determinants modulating metabolic outcomes in a non-human primate model
Creators: name: Newman, Tiffany M.
name: Shively, Carol A.
name: Register, Thomas C.
name: Appt, Susan E.
name: Hariom Yadav
name: Colwell, Rita R.
name: Fanelli, Brian
name: Dadlani, Manoj
name: Karlis Graubics
name: Nguyen, Uyen Thao
name: Sivapriya Ramamoorthy
name: Uberseder, Beth
name: Kenysha Y. J. Clear
name: Wilson, Adam S.
name: Reeves, Kimberly D.
name: Chappell, Mark C.
name: Tooze, Janet A.
name: Cook, Katherine L.
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Genetics
subject: Physiology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: Ecology
subject: Inorganic Chemistry
subject: Computational Biology
subject: Cardiology

description: Additional file 1: Supplemental Table 1. Non-human primate diets replicating human Western and Mediterranean dietary patterns. Supplemental Figure S1. Individual read statistics on each sample. Samples ranged from 13,694,588 to 28,756,486 reads with no significant differences in reads between dietary patterns. Supplemental Figure S2. Diet, not pen effects, drive microbiome populations. A. PCoA of bacterial beta diversity based on the Bray-Curtis dissimilarity; different solid color spheres indicates subjects housed in same pen. B. Shannon diversity of each subject; different solid color spheres indicates subjects housed in same pen. Supplemental Figure S3. Diet shifts viral and protozoa populations in the gut microbiome. A. Relative abundance of viral species in different fecal samples is visualized by bar plots. Samples are aggregated by diet cohort. Each colored box represents a viral species. The height of a color box represents the relative abundance of that organism within the sample. “Other” represents lower abundance taxa (&lt;5%). B. Relative abundance of protozoa species in different fecal samples is visualized by bar plots. Samples are aggregated by diet cohort. Each colored box represents a protist species. The height of a color box represents the relative abundance of that organism within the sample. “Other” represents lower abundance taxa (&lt;5%). C. Relative abundance of fungal species in different fecal samples is visualized by bar plots. Samples are aggregated by diet cohort. Each colored box represents a fungal species. The height of a color box represents the relative abundance of that organism within the sample. “Other” represents lower abundance taxa (&lt;5%). D. A. Relative abundance of phages in different fecal samples is visualized by bar plots. Samples are aggregated by diet cohort. Each colored box represents a bacteriophage species. The height of a color box represents the relative abundance of that organism within the sample. “Other” represents lower abundance taxa (&lt;5%). Supplemental Figure S4. Western diet-fed subjects with low P. copri abundance display elevated plasma gamma-glutamyl amino acid and phosphatidylethanolamine metabolites. Supplemental Figure S5. Obesity regardless of diet does not significantly regulate the gut microbiome. A. Shannon diversity. B. PCoA of bacterial beta diversity based on the Bray-Curtis dissimilarity. C. Relative abundance of bacterial species in different fecal samples is visualized by bar plots. Each bar represents a subject and each colored box a bacterial taxon. The height of a color box represents the relative abundance of that organism within the sample. “Other” represents lower abundance taxa. D. Proportional abundance of Treponema (Genus) in obese and lean NHP regardless of dietary pattern. E. Proportional abundance of Treponema succinifaciens in obese and lean NHP regardless of dietary pattern.