Table 3 Functional metabolic genes and pathways affected per storage condition as compared to fresh samples
From: Sample storage conditions induce post-collection biases in microbiome profiles
Condition | Genesa | Pathwaysb | |||||
|---|---|---|---|---|---|---|---|
Number | % | Number | % | Greatest change | Log2FC | p value | |
Fresh | 5110 | 100 | 276 | 100 | NA | NA | NA |
EDTA | 978 | 19.1 | 27 | 9.8 | Toluene degradation | + 3.9 | < 0.0003 |
Lysis | 689 | 13.5 | 40 | 14.5 | Toluene degradation | + 4.5 | < 0.0006 |
RT | 1050 | 20.5 | 40 | 14.5 | Lysine degradation | −2.1 | < 0.003 |
4 °C | 3533 | 69.1 | 198 | 71.7 | Apoptosis | + 3.2 | < 0.00001 |
−20 °C | 2637 | 51.6 | 183 | 66.3 | Alzheimer Disease | −1.9 | < 0.0006 |
−80 °C | 1088 | 21.3 | 50 | 18.1 | Beta-lactam resistance | −2.0 | < 0.005 |
HY | 3317 | 64.9 | 176 | 63.8 | Fatty acid biosynthesis | + 5.3 | < 0.0003 |
Pathways not affected | 22 | 8.0 | NA | NA | NA | ||
Affected by all conditions | 0 | 0 | none | NA | NA | ||
Pathway affected by 6 out of 7 conditions (excludes EDTA) | 1 | 0.4 | Tyrosine metabolism | varies | varies | ||