Table 3.
Wilcoxon and NBMM Analyses to Examine Changes in Select Taxa Abundance Between Baseline and Final Fecal Sample by Chemotherapy Treatment: neoADJ vs. Non-neoADJ (ADJ+ noC)
| Mean Baseline (B) and Absolute Changes (Δ) in Taxa Abundance by Chemotherapy | neoADJ vs. Non-neoADJ | |||||||
|---|---|---|---|---|---|---|---|---|
| All N = 33 | neoADJ N = 16 | ADJ N = 13 | noC N = 4 | Wilcoxon Test a | NBMMb | |||
| No BMI Adjustment | BMI Adjustment | |||||||
| Specific taxa | N = 33 | N = 33 | N = 33 | |||||
| P__Actinobacteria | B | 0.013 (0.005) | 0.013 (0.005) | 0.017 (0.011) | 0 (0) | 0.55 | ||
| f__Micrococcaceae | Change | −0.006(0.006) | −0.01 (0.003) | −0.006(0.013) | 0.007 (0.007) | 0.11 | ||
| g_Rothia | Pc | 0.20 | 0.008 | 1.00 | 0.50 | 0.11 | 0.16 | |
| P__Actinobacteria | B | 0.292 (0.086) | 0.202 (0.11) | 0.359 (0.137) | 0.313 (0.311) | 0.44 | ||
| f__Coriobacteriaceae | Change | 0.138 (0.121) | −0.045 (0.13) | 0.359(0.214) | −0.149 (0.146) | 0.64 | ||
| g_ Slackia | Pc | 0.37 | 0.84 | 0.21 | 0.25 | 0.002 | 0.00036 | |
| P_ Bacteroidetes | B | 0.014(0.005) | 0.003(0.003) | 0.026(0.011) | 0.014 (0.014) | 0.02 | ||
| f_ Rikenellaceae | Change | 0.012(0.008) | 0.025(0.012) | −0.006(0.01) | 0.017(0.017) | 0.10 | ||
| Pc | 0.14 | 0.03 | 0.73 | 1.00 | 0.001 | 0.00037 | ||
| P_Bacteroidetes | B | 0.791(0.179) | 0.793(0.203) | 0.683(0.244) | 1.135(1.08) | 0.41 | ||
| f_ Rikenellaceae | Change | 0.036(0.008) | 0.228(0.218) | −0.114(0.219) | −0.249(0.213) | 0.76 | ||
| g_ | Pc | 0.92 | 0.50 | 0.91 | 0.25 | 0.033 | 0.063 | |
| P__Bacteroidetes | B | 0.026 (0.009) | 0.035 (0.015) | 0.013(0.012) | 0.033 (0.02) | 0.056 | ||
| f_Rikenellaceae | Change | −0.012 (0.009) | −0.032 (0.015) | 0.014(0.008) | −0.014 (0.008) | 0.007 | ||
| g_Alistipes | Pc | 0.19 | 0.016 | 0.25 | 0.50 | 0.000033 | 0.000033 | |
| P_Bacteroidetes | B | 0.26 (0.10) | 0.25 (0.17) | 0.35 (0.16) | 0 (0) | 0.37 | ||
| f_ S24-7 | Change | −0.17(0.09) | −0.11 (0.16) | −0.31(0.13) | 0.01 (0.01) | 0.12 | ||
| g_ | Pc | 0.12 | 0.91 | 0.020 | 0.50 | 0.00039 | 0.008 | |
| P__Euryarchaeota | B | 1.242 (0.87) | 2.087 (1.78) | 0.366 (0.26) | 0.711 (0.71) | 0.92 | ||
| f_Methanobacteriaceae | Change | −0.696 (0.59) | −1.428 (1.17) | −0.202 (0.29) | 0.624 (0.59) | 0.80 | ||
| g__Methanobrevibacter | Pc | 0.55 | 0.16 | 0.74 | 0.25 | 0.003 | 0.003 | |
| P_Firmicutes | B | 0.006 (0.002) | 0.005 (0.002) | 0.009 (0.003) | 0.002 (0.002) | 0.36 | ||
| f_ Gemellaceae | Change | 0.002 (0.004) | 0.007 (0.006) | −0.003 (0.004) | 0 (0.003) | 0.36 | ||
| g_ | Pc | 0.74 | 0.82 | 0.43 | 1.00 | 0.005 | 0.006 | |
| P_Firmicutes | B | 0.137 (0.06) | 0.14 (0.09) | 0.16 (0.11) | 0.06 (0.06) | 0.62 | ||
| f_ Enterococcaceae | Change | 0.014 (0.13) | 0.13 (0.27) | −0.12(0.09) | −0.02(0.03) | 0.26 | ||
| g_Enterococcus | Pc | 0.18 | 0.92 | 0.047 | 0.75 | 0.028 | 0.035 | |
| P_Firmicutes | B | 0.042 (0.022) | 0.003 (0.002) | 0.05 (0.031) | 0.17 (0.15) | 0.13 | ||
| f_Turicibacteraceae | Change | −0.016 (0.02) | 0.014 (0.009) | −0.023 (0.04) | −0.11(0.10) | 0.26 | ||
| g_Turicibacter | Pc | 0.90 | 0.15 | 0.69 | 0.13 | 0.001 | 0.001 | |
| P_ Firmicutes | B | 0.095 (0.07) | 0.013 (0.01) | 0.20 (0.18) | 0.08 (0.08) | 0.70 | ||
| f_ Clostridiaceae | Change | −0.043 (0.07) | 0.077 (0.05) | −0.19 (0.17) | −0.04 (0.06) | 0.28 | ||
| g_ | Pc | 0.72 | 0.34 | 0.69 | 1.00 | 0.003 | 3.3 E-10 | |
| P_ Firmicutes | B | 0.104(0.06) | 0.048(0.03) | 0.032 (0.03) | 0.567 (0.46) | 0.16 | ||
| f_ Lachnospiraceae | Change | 0.019 (0.06) | −0.040(0.03) | 0.198 (0.12) | −0.328 (0.24) | 0.003 | ||
| g_ Clostridium | Pc | 0.76 | 0.38 | 0.024 | 0.13 | 0.017 | 0.027 | |
| P_ Firmicutes | B | 1.50 (0.26) | 1.55 (0.45) | 1.45 (0.31) | 1.41 (0.85) | 0.63 | ||
| f_ Ruminococaceae | Change | 0.06 (0.24) | 0.51 (0.30) | −0.42(0.44) | −0.22(0.27) | 0.13 | ||
| g_ | Pc | 0.69 | 0.14 | 0.50 | 0.63 | 0.036 | 0.048 | |
| P_ Firmicutes | B | 0.44 (0.24) | 0.87 (0.48) | 0.033 (0.03) | 0.036 (0.04) | 0.40 | ||
| f_ Veillonellaceae | Change | 0.056 (0.33) | −0.41 (0.55) | 0.626 (0.46) | 0.072 (0.06) | 0.31 | ||
| g_ Acidaminoccoccus | Pc | 0.30 | 0.84 | 0.13 | 0.50 | 0.001 | 0.001 | |
| P__Firmicutes | B | 0.038 (0.021) | 0.05 (0.041) | 0.034 (0.016) | 0.001 (0.001) | 0.62 | ||
| f_ Mogibacteriaceae | Change | −0.002 (0.21) | 0.018 (0.04) | −0.029 (0.016) | 0.008 (0.007) | 0.26 | ||
| g_ Mogibacterium | Pc | 0.80 | 0.69 | 0.16 | 0.50 | 0.049 | 0.062 | |
| P__Firmicutes | B | 0.143 (0.062) | 0.094 (0.066) | 0.247 (0.134) | 0.001 (0.001) | 0.52 | ||
| f_ Erysipelotrichaceae | Change | −0.012 (0.08) | 0.169 (0.106) | −0.241 (0134) | 0.005 (0.006) | 0.09 | ||
| g__Catenibacterium | Pc | 0.93 | 0.16 | 0.13 | 1.00 | 7.0 E-06 | 0.24 | |
| P__Firmicutes | B | 0.37 (0.11) | 0.09(0.03) | 0.80 (0.24) | 0.10 (0.09) | 0.032 | ||
| f_ Erysipelotrichaceae | Change | −0.13(0.11) | 0.16(0.07) | −0.57(0.23) | 0.12(0.08) | 0.003 | ||
| g__[Eubacterium] | Pc | 0.95 | 0.042 | 0.020 | 0.13 | 0.00048 | 0.001 | |
| P__Proteobacteria | B | 0.092(0.02) | 0.133(0.033) | 0.042(0.012) | 0.085(0.074) | 0.08 | ||
| f_ Desulfovibrionaceae | Change | 0.086(0.059) | 0.019(0.047) | 0.214(0.132) | −0.062(0.063) | 0.006 | ||
| g__Bilophila | Pc | 0.23 | 0.50 | 0.002 | 0.75 | 0.015 | 0.019 | |
| P__Proteobacteria | B | 0.356(0.16) | 0.431(0.29) | 0.37(0.23) | 0.009(0.008) | 0.39 | ||
| f_ Pasteurellaceae | Change | −0.18(0.17) | −0.16(0.031) | −0.32(0.23) | 0.128(0.096) | 0.03 | ||
| g__Haemophilus | Pc | 0.76 | 0.21 | 0.23 | 0.25 | 0.54 | 0.60 | |
| P_Verrucomicrobia | B | 0.491 (0.371) | 0.976 (0.758) | 0.042 (0.036) | 0.008 (0.006) | 0.018 | ||
| f_ Verrucomicrobiaceae | Change | −0.138 (0.407) | −0.738 (0.784) | 0.370 (0.277) | 0.605 (0.578) | 0.15 | ||
| g_ Akkermansia | Pc | 0.52 | 0.45 | 0.16 | 0.50 | 0.005 | 0.008 | |
Notes: aWilcoxon rank sum (1df) comparing neoADJ vs. non-neoADJ (ADJ + noC) groups at baseline and last collections, and in the change between last and baseline samples. bNegative binomial mixed model tests in R: glmm.nb (count at gena ~ period*weight change2 + offset(log(totreads)), random = ~ 1|SubjectID), Period (final vs. baseline), t change2 (increase weight vs. decrease weight). Age (continuous), race (Hispanic or not Hispanic), and total number of reads were included in the models. cWilcoxon signed rank (1df) to test changes between last and baseline samples.