Supplementary File 2:
Differences in Average Pre-Transplant Taxa Abundances Between Donors and Recipients
The Welch two-group t-test was used to evaluate which taxa (collapsed at the species taxonomic level, then log-transformed) differed on average between allo-HSCT recipients (N = 57) and donors (N = 22) at baseline. We used the Benjamini-Hochberg1 false discovery rate (FDR) procedure for multiple test correction. We tested a total of 103 taxa, with 170 omitted from testing due to pre-processing criteria (only observed in less than 15% of subjects or less than 0.1% maximum relative abundance among subjects. We found 58 taxa to differ in mean relative abundance between the two groups (Table S1).
Because of our relatively low sample size and the skewed distributions of taxa relative abundances, weconsidered presenting instead a non-parametric analogue instead of the Welch t-test with log-transformation. However, rejection (i.e., P < 0.05, FDR < 0.20) of a test like the Mann-Whitney U is arguably more difficult to interpret in this setting, as the null hypothesis tests whether the distribution between the two groups differs2, including a sensitivity to both scale (variance) and location (mean) differences. As there is qualitativelymuch highervariability in the microbiota of recipients than donors (main text, Figure 1), we felt that the non-parametric testshad less informative null hypotheses than that of the t-test.
Table S1: Taxa with different mean relative abundances between allo-HSCT recipients and donors. Relative abundance (RA) is presented as a percentage (0% - 100%). The rows (i.e., the taxa, presented as “Order > Family > Genus > Species”) are sorted by effect size (mean difference: mean recipient abundance minus mean donor abundance)
.
MeanRA, Recipients / Mean RA, Donors / Mean Difference / p-value / FDRTaxa Comparatively Decreased in Allo-HSCT Recipients
Bacteroidales > Bacteroidaceae > Bacteroides > unknown / 4.18E+0 / 1.69E+1 / -1.27E+1 / 7.09E-4 / 5.29E-3
Clostridiales > Lachnospiraceae > unknown > unknown / 5.49E+0 / 9.89E+0 / -4.40E+0 / 2.58E-2 / 8.30E-2
Clostridiales > Ruminococcaceae > unknown > unknown / 2.90E+0 / 6.24E+0 / -3.34E+0 / 1.79E-2 / 6.35E-2
Clostridiales > unknown > unknown > unknown / 1.44E+0 / 3.81E+0 / -2.37E+0 / 1.05E-3 / 6.74E-3
Clostridiales > Lachnospiraceae > Blautia > unknown / 1.69E+0 / 3.33E+0 / -1.64E+0 / 5.65E-2 / 1.24E-1
Clostridiales > Ruminococcaceae > Faecalibacterium > prausnitzii / 6.44E-2 / 1.39E+0 / -1.32E+0 / 2.74E-7 / 9.39E-6
Bacteroidales > Bacteroidaceae > Bacteroides > uniformis / 3.00E-1 / 1.52E+0 / -1.22E+0 / 4.14E-2 / 1.04E-1
Clostridiales > Lachnospiraceae > Coprococcus > unknown / 3.01E-1 / 1.50E+0 / -1.20E+0 / 2.45E-5 / 2.80E-4
Clostridiales > Ruminococcaceae > Ruminococcus > unknown / 9.03E-1 / 2.01E+0 / -1.11E+0 / 5.36E-2 / 1.23E-1
Clostridiales > Lachnospiraceae > Roseburia > unknown / 1.92E-1 / 9.04E-1 / -7.11E-1 / 5.18E-3 / 2.37E-2
Bacteroidales > Rikenellaceae > unknown > unknown / 8.00E-2 / 5.07E-1 / -4.27E-1 / 1.56E-3 / 7.75E-3
Clostridiales > Lachnospiraceae > [Ruminococcus] > unknown / 2.12E-1 / 4.94E-1 / -2.82E-1 / 1.08E-1 / 1.92E-1
Bacteroidales > Porphyromonadaceae > Parabacteroides > distasonis / 7.92E-2 / 3.49E-1 / -2.70E-1 / 7.03E-2 / 1.48E-1
Clostridiales > Clostridiaceae > unknown > unknown / 5.88E-2 / 1.94E-1 / -1.35E-1 / 5.07E-2 / 1.23E-1
Clostridiales > Veillonellaceae > Phascolarctobacterium > unknown / 8.63E-3 / 1.24E-1 / -1.15E-1 / 9.30E-3 / 3.99E-2
Clostridiales > Lachnospiraceae > Lachnospira > unknown / 2.32E-3 / 1.10E-1 / -1.07E-1 / 1.29E-5 / 1.90E-4
Burkholderiales > Alcaligenaceae > Sutterella > unknown / 5.34E-4 / 8.90E-2 / -8.84E-2 / 4.54E-7 / 1.17E-5
Clostridiales > Clostridiaceae > Clostridium > unknown / 3.39E-3 / 8.34E-2 / -8.00E-2 / 2.43E-5 / 2.80E-4
Coriobacteriales > Coriobacteriaceae > Collinsella > aerofaciens / 1.04E-3 / 4.19E-2 / -4.08E-2 / 1.54E-3 / 7.75E-3
Clostridiales > [Mogibacteriaceae] > unknown > unknown / 5.63E-4 / 3.06E-2 / -3.00E-2 / 1.09E-9 / 1.12E-7
Clostridiales > Christensenellaceae > unknown > unknown / 7.41E-4 / 2.96E-2 / -2.88E-2 / 8.06E-6 / 1.38E-4
Clostridiales > Lachnospiraceae > Anaerostipes > unknown / 3.19E-4 / 1.95E-2 / -1.92E-2 / 1.07E-4 / 1.00E-3
Bacteroidales > Bacteroidaceae > Bacteroides > caccae / 3.39E-3 / 2.14E-2 / -1.80E-2 / 7.60E-2 / 1.54E-1
Coriobacteriales > Coriobacteriaceae > unknown > unknown / 2.30E-3 / 1.79E-2 / -1.56E-2 / 1.27E-2 / 5.24E-2
Bacteroidales > Bacteroidaceae > Bacteroides > fragilis / 3.66E-3 / 1.56E-2 / -1.19E-2 / 8.51E-2 / 1.69E-1
Bifidobacteriales > Bifidobacteriaceae > Bifidobacterium > adolescentis / 1.12E-3 / 1.07E-2 / -9.50E-3 / 2.95E-2 / 8.69E-2
Coriobacteriales > Coriobacteriaceae > Collinsella > unknown / 4.36E-4 / 9.83E-3 / -9.40E-3 / 5.30E-3 / 2.37E-2
Bacteroidales > [Odoribacteraceae] > Odoribacter > unknown / 2.77E-4 / 8.89E-3 / -8.60E-3 / 1.40E-3 / 7.75E-3
Erysipelotrichales > Erysipelotrichaceae > Holdemania > unknown / 8.49E-5 / 8.00E-3 / -7.90E-3 / 3.70E-8 / 1.91E-6
Desulfovibrionales > Desulfovibrionaceae > Bilophila > unknown / 1.12E-4 / 6.33E-3 / -6.20E-3 / 7.19E-4 / 5.29E-3
Coriobacteriales > Coriobacteriaceae > Adlercreutzia > unknown / 7.62E-5 / 5.66E-3 / -5.60E-3 / 1.01E-6 / 2.09E-5
Coriobacteriales > Coriobacteriaceae > Eggerthella > lenta / 1.43E-3 / 6.20E-3 / -4.80E-3 / 3.57E-2 / 9.44E-2
Bacteroidales > Prevotellaceae > Prevotella > unknown / 5.61E-4 / 4.27E-3 / -3.70E-3 / 3.41E-2 / 9.42E-2
Clostridiales > Lachnospiraceae > Roseburia > faecis / 6.27E-4 / 3.25E-3 / -2.60E-3 / 5.31E-2 / 1.23E-1
Clostridiales > Lachnospiraceae > Dorea > formicigenerans / 1.91E-4 / 2.37E-3 / -2.20E-3 / 2.07E-2 / 6.88E-2
Clostridiales > Lachnospiraceae > Lachnobacterium > unknown / 3.71E-4 / 2.56E-3 / -2.20E-3 / 3.41E-2 / 9.42E-2
Pasteurellales > Pasteurellaceae > Haemophilus > parainfluenzae / 4.06E-4 / 2.17E-3 / -1.80E-3 / 1.05E-1 / 1.90E-1
Bacteroidales > [Odoribacteraceae] > Butyricimonas > unknown / 1.08E-4 / 1.29E-3 / -1.20E-3 / 3.48E-2 / 9.42E-2
Bacteroidales > [Paraprevotellaceae] > Paraprevotella > unknown / 8.70E-5 / 9.90E-4 / -9.00E-4 / 5.28E-2 / 1.23E-1
Desulfovibrionales > Desulfovibrionaceae > Desulfovibrio > unknown / 4.85E-5 / 6.43E-4 / -6.00E-4 / 1.98E-2 / 6.80E-2
Coriobacteriales > Coriobacteriaceae > Slackia > unknown / 5.51E-5 / 3.38E-4 / -3.00E-4 / 1.02E-1 / 1.88E-1
Bacteroidales > Bacteroidaceae > Bacteroides > coprophilus / 1.83E-5 / 2.22E-4 / -2.00E-4 / 6.40E-2 / 1.37E-1
Clostridiales > Christensenellaceae > Christensenella > unknown / 1.94E-5 / 2.27E-4 / -2.00E-4 / 1.72E-2 / 6.31E-2
Coriobacteriales > Coriobacteriaceae > Collinsella > stercoris / 4.06E-5 / 2.37E-4 / -2.00E-4 / 9.04E-2 / 1.73E-1
RF32 > unknown > unknown > unknown / 1.52E-5 / 2.48E-4 / -2.00E-4 / 2.66E-2 / 8.30E-2
Bacteroidales > Porphyromonadaceae > Porphyromonas > unknown / 3.19E-5 / 1.46E-4 / -1.00E-4 / 1.02E-1 / 1.88E-1
Clostridiales > Dehalobacteriaceae > Dehalobacterium > unknown / 2.98E-5 / 1.71E-4 / -1.00E-4 / 7.58E-2 / 1.54E-1
Erysipelotrichales > Erysipelotrichaceae > Catenibacterium > unknown / 1.24E-5 / 1.25E-4 / -1.00E-4 / 8.70E-2 / 1.69E-1
Taxa Comparatively Increased in Allo-HSCT Recipients
Lactobacillales > Lactobacillaceae > Pediococcus > acidilactici / 3.50E-5 / 3.31E-6 / 1.90E-6 / 1.52E-2 / 5.81E-2
Lactobacillales > Enterococcaceae > Enterococcus > casseliflavus / 1.83E-4 / 1.33E-5 / 2.00E-4 / 1.58E-3 / 7.75E-3
Lactobacillales > Lactobacillaceae > Lactobacillus > zeae / 5.92E-4 / 4.41E-5 / 5.00E-4 / 1.45E-3 / 7.75E-3
Lactobacillales > Enterococcaceae > unknown > unknown / 7.33E-4 / 4.33E-5 / 7.00E-4 / 9.39E-4 / 6.45E-3
Lactobacillales > Enterococcaceae > Enterococcus > unknown / 6.04E-3 / 9.86E-5 / 5.90E-3 / 4.99E-5 / 5.14E-4
Actinomycetales > Actinomycetaceae > Actinomyces > unknown / 1.89E-2 / 6.52E-3 / 1.24E-2 / 5.63E-2 / 1.24E-1
Erysipelotrichales > Erysipelotrichaceae > [Eubacterium] > dolichum / 2.46E-2 / 5.49E-3 / 1.91E-2 / 3.93E-2 / 1.01E-1
Lactobacillales > Lactobacillaceae > Lactobacillus > unknown / 2.01E-2 / 3.98E-4 / 1.97E-2 / 1.38E-4 / 1.18E-3
Clostridiales > Lachnospiraceae > Blautia > producta / 1.60E-1 / 2.69E-2 / 1.33E-1 / 2.78E-2 / 8.41E-2
Lactobacillales > Streptococcaceae > Streptococcus > unknown / 1.24E+0 / 4.56E-1 / 7.82E-1 / 1.33E-2 / 5.27E-2
References
1 Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B. 1995; 57: 289–300.
2 Fagerland MW. T-tests, non-parametric tests, and large studies—a paradox of statistical practice? BMC Med Res Methodol 2012; 12: 78.