Supplementary material for:
Biotic interactions and temporal dynamics of the human gastrointestinal microbiota
Pål Trosvik 1*
, Eric Jacques de Muinck
1
and Nils Christian Stenseth
1
1. Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, Faculty of
Mathematics and Natural Sciences, University of Oslo.
*Correspondence to Pål Trosvik: pal.trosvik@ibv.uio.no
Supplementary figures S1-S9

Figure S1 . Shannon entropy over time, as measured for genus level OTUs, for the male (black) and female (red) subject, computed from data subsampled to the lowest number of sequence reads (Table 1). The dotted lines are means. The mean and the variance are elevated in the male relative to the female (p<<0.001, t.test and Levene’s test, respectively).

Figure S2 .Richness over time. The black and red curves are for the male and the female, respectively.
The dashed lines are means. A.
Number of observed genus level OTUs (richness) from raw OTU counts. The means are significantly different but not the variances (p<<0.001, t-test and p = 0.46
Levene’s test, respectively).
B.
Number of observed genus level OTUs from data subsampled to the lowest sequencing depth (Table 1). The means are significantly different but not the variances
(p<<0.001, t-test and p = 0.63 Levene’s test, respectively) .

Figure S3.
Shannon entropy vs. sequencing depth. Black and red are for raw genus level
OTU counts and data subsampled to the lowest number of sequences (Table 1), respectively.
There are significant positive correlations in both data sets (p<0.025, linear models; p<0.026,
Spearman’s correlation tests).

Figure S4.
Box-and-whisker plots of Pielou’s evenness indices. This metric is computed as the ratio between the observed Shannon entropy in a sample and the Shannon entropy of a community with the same richness and perfect evenness, with a value of 1 indicating a perfectly even community in the sample. Boxes represent the interquartile range (i.e. 50% of the data). Fat black lines in boxes are medians. Whiskers are 1.5 times the interquartile range.
A) Raw genus level OTU count data. Means and variances differ significantly between the subjects (p<<0.001, t-test and Levene’s test, respectively). B) Genus level OTU data subsampled to the lowest sequencing depth (Table 1). Means and variances differ significantly between the subjects (p<<0.001, t-test and Levene’s test, respectively).

Figure S5 . Relationships between specific phylum abundances and genus level OTU Shannon entropy using data subsampled to the lowest sequencing depth (Table 1). The green (Bacteroidetes) and blue (Firmicutes) lines are linear regression fits. Turquoise (Actinobacteria) and pink
(Proteobacteria) lines are smoothing splines fitted with three degrees of freedom (regressions fitted with generalized additive models). All regression fits are highly significant (p<<0.001).

Figure S6 . Relationships between specific phylum abundances and genus level OTU counts. The green (Bacteroidetes) and blue (Firmicutes) lines are linear regression fits. Turquoise
(Actinobacteria) and pink (Proteobacteria) lines are smoothing splines fitted with three degrees of freedom (regressions fitted with generalized additive models). All regression fits are highly significant (p<<0.001).

Figure S7 . Relationships between specific phylum abundances and genus level OTU counts using data subsampled to the lowest sequencing depth (Table 1). The green (Bacteroidetes) and blue
(Firmicutes) lines are linear regression fits. Turquoise (Actinobacteria) and pink
(Proteobacteria) lines are smoothing splines fitted with three degrees of freedom (regressions fitted with generalized additive models). All regression fits are highly significant (p<<0.001).

Figure S8 . Relationships between specific phylum abundances and Pielou’s evenness index for genus level OTUs. The green (Bacteroidetes) and blue (Firmicutes) lines are linear regression fits.
Turquoise (Actinobacteria) and pink (Proteobacteria) lines are smoothing splines fitted with three degrees of freedom (regressions fitted with generalized additive models). All regression fits are highly significant (p<<0.001).

Figure S9 . Relationships between specific phylum abundances and Pielou’s evenness index for genus level OTUs, using data subsampled to the lowest sequencing depth (Table 1). The green
(Bacteroidetes) and blue (Firmicutes) lines are linear regression fits. Turquoise
(Actinobacteria) and pink (Proteobacteria) lines are smoothing splines fitted with three degrees of freedom (regressions fitted with generalized additive models). All regression fits are highly significant (p<<0.001).