Table 2.
Pair-wise | base mean | Log2 fold change | lfcSE | stat | p value | p adjusted | Genus |
---|---|---|---|---|---|---|---|
High | 33.90 | 11.12 | 2.85 | 3.90 | 9.74E-05 | 0.0093 | Klebsiella |
16.16 | 23.66 | 5.92 | 4.00 | 9.74E-05 | 0.0067 | Veillonella* | |
2.59 | 23.04 | 5.92 | 3.89 | 9.93E-05 | 0.009345 | Veillonella* | |
Decreased | 68.40 | −2.89 | 0.84 | −3.45 | 0.0005576 | 0.03653 | Romboutsia |
40.17 | −4.74 | 1.24 | −3.83 | 0.000128 | 0.011178 | Enterococcus | |
36.80 | −3.37 | 0.75 | −4.49 | 7.13E-06 | 0.001006 | Intestinibacter | |
High | 91.95 | 19.79 | 5.84 | 3.39 | 0.0007063 | 0.023203 | Veillonella* |
33.90 | 9.69 | 2.87 | 3.37 | 0.0007523 | 0.024312 | Klebsiella | |
16.16 | 35.34 | 5.97 | 5.92 | 3.14E-09 | 5.95E-07 | Veillonella* | |
Neutral | 68.40 | −2.88 | 0.84 | −3.40 | 0.0006627 | 0.021951 | Romboutsia |
40.17 | –4.42 | 1.25 | −3.55 | 0.0003914 | 0.013917 | Enteroccocus | |
36.80 | −3.86 | 0.76 | −5.10 | 3.43E-07 | 4.40E-05 | Intestinibacter | |
High | 91.95 | 23.27 | 5.98 | 3.89 | 9.97E-05 | 0.003386 | Veillonella |
33.90 | 11.17 | 2.94 | 3.79 | 0.0001484 | 0.00458 | Klebsiella | |
17.77 | 13.94 | 4.43 | 3.15 | 0.0016554 | 0.035626 | Phascolarctobacterium | |
Increased | 40.17 | −4.61 | 1.27 | −3.62 | 0.0002916 | 0.007681 | Enterococcus |
20.27 | −2.43 | 0.64 | −3.81 | 0.0001388 | 0.004329 | Lachnoclostridium | |
17.55 | −2.33 | 0.63 | −3.72 | 0.0002009 | 0.005902 | Erysipelatoclostridium | |
Increased | 9.15 | 30.00 | 3.85 | 7.78 | 7.03E-15 | 3.26E-12 | Escherichia/Shigella* |
6.86 | 16.40 | 3.86 | 4.25 | 2.10E-05 | 0.000638 | Escherichia/Shigella* | |
5.84 | 9.63 | 2.42 | 3.98 | 6.90E-05 | 0.002038 | Bacteroides | |
Decreased | 19.75 | −19.63 | 3.86 | −5.09 | 3.53E-07 | 2.00E-05 | Veillonella |
13.36 | −29.79 | 3.86 | −7.72 | 1.12E-14 | 4.15E-12 | Megasphaera | |
6.97 | −6.55 | 1.70 | −3.85 | 0.0001173 | 0.003287 | Klebsiella | |
Increased | 14.13 | 7.69 | 1.71 | 4.49 | 6.96E-06 | 0.000299 | Citrobacter |
5.84 | 10.89 | 2.44 | 4.47 | 8.00E-06 | 0.00034 | Bacteroides | |
3.06 | 27.04 | 3.89 | 6.95 | 3.61E-12 | 3.02E-10 | Escherichia/Shigella | |
Neutral | 267.32 | −2.30 | 0.68 | −3.39 | 0.0007071 | 0.026723 | Bifidobacterium |
19.75 | −16.58 | 3.89 | −4.26 | 2.01E-05 | 0.000822 | Veillonella | |
6.97 | −7.24 | 1.71 | −4.23 | 2.38E-05 | 0.000964 | Klebsiella | |
Neutral | 9.15 | 18.37 | 3.56 | 5.16 | 2.48E-07 | 3.18E-05 | Escherichia/Shigella* |
6.86 | 15.09 | 3.56 | 4.24 | 2.24E-05 | 0.001983 | Escherichia/Shigella* | |
5.81 | 14.73 | 3.56 | 4.14 | 3.50E-05 | 0.002961 | Anaeroglobus | |
Decreased | 13.36 | −28.66 | 3.56 | −8.05 | 8.41E-16 | 8.83E-13 | Megasphaera |
6.20 | −12.57 | 3.56 | −3.53 | 0.0004112 | 0.02818 | Sarcina | |
2.59 | −27.94 | 3.56 | −7.84 | 4.33E-15 | 3.45E-12 | Veillonella |
The top three ASVs by base mean from each group in the pair-wise comparison are listed and described taxonomically at the genus level (n = 403 individual stool samples). Genera indicated with an asterisk (*) represent bacteria shared at the taxonomic level but are actually unique sequences. Breastfeeding status at the time of sample collection was corrected for in the DESeq2 model design. Source data are provided in the source data file