Table 2. Abundance alterations of core bacteriome by seasonal and climatic conditions.
A negative binomial model estimated the association between species abundance of core bacteriome and sampling seasons, GDD- and precipitation level.
| Samples | Species | Mean counts† | Fold change (95% CI) |
q § | Mean counts | Fold change (95% CI) |
q |
|---|---|---|---|---|---|---|---|
| GDD Warmer vs. cooler |
Precipitation More vs. less |
||||||
| May | Bartonella apis | 1068.87 | 0.02 (0, 0.08) | <0.00001 | 1068.87 | 0.99 (0.15, 6.53) | * |
| Bifidobacterium asteroides | 1144.10 | 0.47 (0.31, 0.71) | 0.00274 | 1144.10 | 1.52 (0.94, 2.47) | 0.34335 | |
| Bifidobacterium coryneforme | 180.26 | 0.78 (0.47, 1.3) | 0.55291 | 180.26 | 0.72 (0.43, 1.2) | 0.44555 | |
| Bifidobacterium indicum | 176.76 | 0.81 (0.49, 1.33) | 0.55291 | 176.76 | 0.72 (0.43, 1.19) | 0.44555 | |
| Commensalibacter sp. AMU001 | 162.07 | 0.68 (0.37, 1.25) | 0.46158 | 162.07 | 0.58 (0.32, 1.05) | 0.34335 | |
| Frischella perrara | 3662.30 | 1.18 (0.84, 1.65) | 0.55291 | 3662.30 | 0.97 (0.68, 1.37) | 0.85067 | |
| Gilliamella apicola | 11004.31 | 1.29 (0.94, 1.78) | 0.42005 | 11004.31 | 0.75 (0.55, 1.04) | 0.34335 | |
| Lactobacillus apis | 4366.20 | 0.84 (0.65, 1.09) | 0.46158 | 4366.20 | 1.17 (0.89, 1.54) | 0.47268 | |
| Lactobacillus bombi | 495.19 | 1.03 (0.73, 1.44) | 0.86802 | 495.19 | 0.89 (0.63, 1.26) | 0.67884 | |
| Lactobacillus helsingborgensis | 786.53 | 0.87 (0.71, 1.07) | 0.46158 | 786.53 | 1.2 (0.96, 1.5) | 0.34335 | |
| Lactobacillus kullabergensis | 3454.42 | 1.11 (0.87, 1.41) | 0.55291 | 3454.42 | 0.96 (0.74, 1.24) | 0.80541 | |
| Lactobacillus kunkeei | 187.49 | 3.86 (1.25, 11.89) | 0.09368 | 187.49 | 0.13 (0.05, 0.36) | 0.01120 | |
| Lactobacillus mellis | 213.99 | 1.13 (0.79, 1.61) | 0.62292 | 213.99 | 0.86 (0.59, 1.25) | 0.59928 | |
| Lactobacillus sp. wkB8 | 681.21 | 0.97 (0.8, 1.18) | 0.84023 | 681.21 | 1.1 (0.89, 1.36) | 0.58331 | |
| Snodgrassella alvi | 1706.23 | 0.92 (0.71, 1.2) | 0.62292 | 1706.23 | 0.94 (0.71, 1.24) | 0.78937 | |
| May | Bartonella apis | 1553.31 | 0.28 (0.08, 1.01) | 0.22572 | 1553.31 | 1.46 (0.36, 5.85) | 0.86672 |
| Bifidobacterium asteroides | 942.33 | 0.83 (0.56, 1.22) | 0.74756 | 942.33 | 0.9 (0.6, 1.37) | 0.86672 | |
| Bifidobacterium coryneforme | 79.75 | 0.92 (0.49, 1.73) | 0.98269 | 79.75 | 1.13 (0.59, 2.18) | 0.86672 | |
| Bifidobacterium indicum | 81.39 | 0.9 (0.49, 1.63) | 0.98269 | 81.39 | 1.23 (0.66, 2.28) | 0.86672 | |
| Commensalibacter sp. AMU001 | 255.76 | 0.51 (0.26, 1) | 0.22572 | 255.76 | 0.72 (0.35, 1.49) | 0.86672 | |
| Frischella perrara | 2522.61 | 1.02 (0.66, 1.56) | 0.98269 | 2522.61 | 0.98 (0.62, 1.54) | 0.92494 | |
| Gilliamella apicola | 7869.43 | 1.01 (0.65, 1.57) | 0.98269 | 7869.43 | 1.09 (0.69, 1.73) | 0.86672 | |
| Lactobacillus apis | 1698.58 | 1.62 (1.07, 2.45) | 0.22572 | 1698.58 | 1.23 (0.77, 1.97) | 0.86672 | |
| Lactobacillus bombi | 183.30 | 1.06 (0.68, 1.66) | 0.98269 | 183.30 | 1.03 (0.65, 1.65) | 0.92494 | |
| Lactobacillus helsingborgensis | 952.28 | 1.2 (0.66, 2.17) | 0.98269 | 952.28 | 0.79 (0.43, 1.45) | 0.86672 | |
| Lactobacillus kullabergensis | 1258.90 | 1.5 (0.93, 2.41) | 0.29310 | 1258.90 | 1.17 (0.7, 1.97) | 0.86672 | |
| Lactobacillus kunkeei | 36.06 | 1.08 (0.39, 2.97) | 0.98269 | 36.06 | 1.65 (0.59, 4.57) | 0.86672 | |
| Lactobacillus mellis | 78.82 | 1 (0.65, 1.56) | 0.98269 | 78.82 | 1.12 (0.7, 1.77) | 0.86672 | |
| Lactobacillus sp. wkB8 | 648.44 | 1.33 (0.75, 2.36) | 0.74756 | 648.44 | 0.91 (0.49, 1.66) | 0.86672 | |
| Snodgrassella alvi | 1567.32 | 0.66 (0.43, 1.02) | 0.22572 | 1567.32 | 1.43 (0.9, 2.25) | 0.86672 | |
| May vs. March | |||||||
| All | Bartonella apis | 1538.45 | 15.41 (6.07, 39.17) | <0.00001 | |||
| Bifidobacterium asteroides | 1074.14 | 1.61 (1.16, 2.24) | 0.00837 | ||||
| Bifidobacterium coryneforme | 118.29 | 0.74 (0.52, 1.05) | 0.12117 | ||||
| Bifidobacterium indicum | 118.69 | 0.78 (0.55, 1.11) | 0.18588 | ||||
| Commensalibacter sp. AMU001 | 232.29 | 2.46 (1.7, 3.57) | 0.00001 | ||||
| Frischella perrara | 3046.15 | 1.17 (0.85, 1.61) | 0.34279 | ||||
| Gilliamella apicola | 9304.64 | 1.22 (0.92, 1.62) | 0.18588 | ||||
| Lactobacillus apis | 2740.93 | 0.64 (0.48, 0.86) | 0.00656 | ||||
| Lactobacillus bombi | 309.86 | 0.64 (0.48, 0.84) | 0.00519 | ||||
| Lactobacillus helsingborgensis | 928.22 | 1.7 (1.19, 2.43) | 0.00800 | ||||
| Lactobacillus kullabergensis | 2115.13 | 0.57 (0.43, 0.76) | 0.00056 | ||||
| Lactobacillus kunkeei | 99.88 | 0.64 (0.36, 1.14) | 0.16276 | ||||
| Lactobacillus mellis | 133.69 | 0.64 (0.49, 0.85) | 0.00519 | ||||
| Lactobacillus sp. wkB8 | 680.91 | 1.35 (0.98, 1.87) | 0.10342 | ||||
| Snodgrassella alvi | 1700.90 | 1.49 (1.12, 1.98) | 0.01099 | ||||
†Sequence read counts were normalized by dividing raw counts by DESeq size factors
§FDR-adjusted p-value. FDR adjustment was conducted in each pairwise comparison separately
*DESeq method can’t estimate p-values without outlier replacement