Supporting Information
Figure S1. Comparison of the BaAka gut microbiome against that of the Hadza
(other african Hunter ghatherers), US americans part of the human microbiome
project and italians. Venn diagram showing shared genera between the 4 groups. Only
genera present in 5 or more individuals or totaling more than 5 reads in the data set were
considered. B=BaAka; US=US Americans; H=Hadza, IT=Italian. BaAka share 24 genera
with the Hadza as oppose to 5 and 6 with US and Italians respectively.
Figure S2. Taxa (at family level), driving gut microbiome composition differences
among BaAka, Hadza, americans (HMP) and Italians. (a) Boxplots showing the
relative abundance of indicator taxa. (b) Correspondence analysis (CA) showing
ordination of samples based on indicator taxa at family level (above and table S1),
driving gut microbiome composition differences among the 4 groups. For this analysis
only significant discriminators, based on indicator taxa analysis, were used. Axes 1 and 2
explain 36.2 and 11.4% of the variation respectively.
Table S1. Spearman correlation coefficients (rho) and adjusted (FDR) q-values
showing linear relationships between taxa( at family level) and metabolites.
Both taxa and metabolite relationships were estimated based on relative abundance.
Table S2. Indicator taxa (at family level) significantly enriched in the gut
microbiome of the BaAka, Hadza, US Americans and Italians.
The numbers under each group’s column show relative abundance ± SD. The relative
abundance of taxa significantly more enriched within each group, compared to others, is
highlighted with colors (red=BaAka, orange=Hadza, blue=US and green=Italians) and in
bold. Significance of the indicator value was determined through permutation
(Probability), and significantly abundant taxa were determined based on FDR adjustment
(q-value) and using Kruskal-Wallis tests adjusted for multiple comparisons (P<0.05).
Supplemental note
Metabolite Derivatization, gas chromatography and mas spectrometry (GC/MS)
Dried extracts were derivatized with 80 μl methoxyamine hydrochloride (Aldrich,
USA) (40 mg ml-1 in pyridine) for 60 min at 500C and then with 100 μl MSTFA+1%
TMCS (Thermo Sci., USA) at 700C for 120 min and following 2-hour incubation at room
temperature. Five microliters (5 μL) of the internal standard (hentriacontanoic acid (10
mg ml-1); Sigma, USA) were added to each sample prior to derivatization. Samples were
analyzed on a GC/MS system (Agilent Inc, Palo Alto, CA, USA) consisting of an Agilent
7890 gas chromatograph, an Agilent 5975 mass selective detector, and a HP 7683B
autosampler.
1
Gas chromatography was performed on a ZB-5MS (60m×0.32mm I.D. and
0.25m film thickness) capillary column (Phenomenex, CA, USA). The inlet and MS
interface temperatures were 2500C, and the ion source temperature was adjusted to
2300C. An aliquot of 1 L was injected with the split ratio of 10:1. The helium carrier gas
was kept at a constant flow rate of 2 ml min-1. The temperature program was: 5-min
isothermal heating at 700C, followed by an oven temperature increase of 50C min-1 to
3100C and a final 10 min at 3100C. The mass spectrometer was operated in positive
electron impact mode (EI) at 69.9 eV ionization energy in m/z 30-800 scan range
2
3