Additional file 1 of Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys
Creators: name: Jasinska, Anna J.
name: Dong, Tien S.
name: Venu Lagishetty
name: Katzka, William
name: Jacobs, Jonathan P.
name: Schmitt, Christopher A.
name: Cramer, Jennifer Danzy
name: Dongzhu Ma
name: Coetzer, Willem G.
name: J. Paul Grobler
name: Turner, Trudy R.
name: Freimer, Nelson
name: Pandrea, Ivona
name: Apetrei, Cristian
Publisher: name: figshare
Year: 2020
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine

description: Additional file 1 : Supplementary Figure 1. Geographic origins of study animals. Supplementary Figure 2. Maps of sampling sites. The maps were generated using GPS Visualizer [90] with Google Hybrid Map as a background using Map data © 2020 AfriGIS (Pty) Ltd Imagery© 2020 NASA, TerraMetrix. Supplementary Figure 3. Vaginal microbiome in South African vervets in our study compared to Caribbean-origin vervets and other NHPs based on the Yildrim et al. 2014 data [35]. (A) Average community structure in South African vervets (by SIV status), Caribbean origin vervets and other NHPs [35]. Species demarcation: African vervets (SIV Pos and SIV Neg), free-ranging Caribbean vervets (Vw), captive Caribbean-origin vervets (Vc), mangabeys (M), red colobus (Rc), yellow baboon (Bab), olive baboon (Bc), chimpanzee (Chimp), humans (H), lemurs (L), black howler (Bh). (B) Microbial community structure per individual in South African vervets, (C) Community structure per individual in Caribbean-origin vervets [35]. Supplementary Figure 4. A) PCoA of beta-diversity colored by vaginal pH. Acidic pH is a pH &lt;7 while an alkaline pH is a pH &gt; 7. B) Chao1 and Shannon Index of vaginal samples pH. C) Genus taxonomic plots of vaginal samples by pH. D) Differentially abundant microbial genera in acidic vaginal samples vs. alkaline vaginal samples. Supplementary Figure 5. Geography-related microbiome. (A) PCoA for each body site clustering by province. (B) PCoA for each body site clustering by geographic site. (C) Community structure by province. (D) Community structure by geographic site. Differentially abundant taxa between KZN and FS in (E) rectal and (F) fecal microbiome. Supplementary 6. Genus taxonomic plots of D) fecal, E) rectal, F) penile, and G) vaginal samples by the different biomes. Supplementary Figure 7. PCoA of beta-diversity, Chao1 index and Shannon index by different biomes for (A-C) all samples, (D-F) fecal samples, (G-I) rectal samples, (J-L) penile samples, and (M-O) vaginal samples. Supplementary Figure 8. PCoA plots of beta-diversity and alpha diversity metrics of climate variables. PCoA plots of annual mean temperatures in tertiles (Mean Temp Tertile) and minimum temperature of the coldest month in tertiles (Min Temp Tertile) for all samples (A,B), fecal samples (C,D), rectal samples (E,F), penile samples (G,H), and vaginal samples (I,J). Chao1 and shannon index did not differ by any sample type except for Mean Temp Tertile in penile samples (K,L). *Represents p-value&lt;0.05 between either lowest or mid tertile vs the highest tertile. Supplementary Figure 9. Genus taxonomic plots of the annual mean temperatures in tertiles (Mean Temp Tertile) and minimum temperature of the coldest month in tertiles (Min Temp Tertile) by sample type: (A,B) Feces, (C,D) Rectal, (E,F) Penile, (G,H) Vaginal. Only genera with greater than or equal to 1% abundances is shown *Represents the genera that were statistically different between the highest tertile and the lowest tertile adjusting for multiple comparison. Supplementary Figure 10. Sex-related gut microbiome. Differentially abundant taxa in males compared to females in feces (A) and in rectum (B). Supplementary Figure 11. Age-related microbiome. Microbial community structure for each body site. A) Rectal, C) Penile, D) Fecal, E) Vaginal. B) Differentially abundant genera between the rectal microbiome in infants and adults. Supplementary Figure 12. Association of immune biomarkers with microbial taxa in fecal microbiome. Supplementary Figure 13. PCoA of microbial taxa in all samples colored by SIV positive/SIV negative status. Supplementary Figure 14. Differentially abundant microbial genera in chronic vs. acute SIV infection by body site. Analysis was adjusted for sex, age, and vervet location. Penile samples did not show any genera that were significantly different between acute and chronic SIV states after adjusting for other covariates. Supplementary Figure 15. Microbial composition (depicted by heat maps) in SIV negative, SIV acutely infected and SIV chronically infected individuals at four body sites. Microbiome samples comprise of fecal samples (11 SIV negative, 4 acutely infected, 23 chronically infected), rectal samples (41 SIV negative, 11 acutely infected, 43 chronically infected), vaginal samples (10 SIV negative, 6 acutely infected, 30 chronically infected), and penile samples (9 SIV negative, 2 acutely infected, 8 chronically infected). Only genera with a relative abundance &gt; 0.5% are shown. Supplementary Figure 16. Comparison of rectal microbiome community structure between vervets from Caribbean populations and Caribbean-origin captive vervets on Western-style diet (based on data from Amato et al. 2015 [34]) and SIV negative and SIV positive vervets from South Africa.