Table 2. Relative proportions of selected OTUs in the honeybee microbiome.
The following codes were used for the different sample types: (i) EFB0—control bees from outside of the EFB zone without signs of EFB; (ii) EFB1—bees from an EFB apiary, but from colonies without clinical symptoms; and (iii) EFB2—bees from colonies with clinical symptoms of EFB. The sequences were analyzed using METASTATS, and P-values are presented. The OTUs are described according to the closest match in GenBank, and the numbers in brackets indicate the % identity. P-values in bold indicate a statistically significant effect of the EFB factor, with a p value of less than 0.05.
| OTU97 | GenBank identification | aOTU | Mean decrease accuracy | EFB factor | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EFB2 | EFB1 | EFB0 | P-values | |||||||||
| Mean | %stderr | Mean | %stderr | Mean | %stderr | EFB2 EFB1 | EFB2 EFB0 | EFB1 EFB0 | ||||
| OTU4 | Melissococcus plutonius (99) | 13,112 | 1.361 | 0.03055 | 23.1 | 0.00046 | 19.3 | 0.00012 | 54.8 | 0.001 | 0.000 | 0.011 |
| OTU5 | Fructobacillus fructosus (99) | 9,845 | 0.737 | 0.02272 | 36.0 | 0.00133 | 49.1 | 0.00006 | 50.8 | 0.028 | 0.000 | 0.079 |
| OTU109 | Lactobacillus kimbladii (99) | 2,668 | 0.313 | 0.00296 | 7.1 | 0.00487 | 20.6 | 0.00264 | 21.4 | 0.096 | 0.598 | 0.079 |
| OTU9 | Lactobacillus kunkeei (99) | 5,679 | 0.275 | 0.01260 | 39.6 | 0.00045 | 21.8 | 0.00077 | 82.6 | 0.040 | 0.002 | 0.714 |
| OTU8 | Lactobacillus mellis (99) | 44,528 | 0.273 | 0.06059 | 8.7 | 0.05986 | 16.5 | 0.03653 | 19.3 | 0.962 | 0.010 | 0.083 |
| OTU6 | Snodgrassella alvi (99) | 101,925 | 0.269 | 0.12245 | 8.2 | 0.22007 | 11.4 | 0.07790 | 12.8 | 0.003 | 0.003 | 0.000 |
| OTU7 | Lactobacillus helsingborgensis (99) | 61,676 | 0.245 | 0.07324 | 12.4 | 0.10213 | 5.9 | 0.05802 | 10.8 | 0.025 | 0.183 | 0.000 |
| OTU12 | Lactobacillus kullabergensis (99) | 26,246 | 0.243 | 0.02732 | 9.0 | 0.04641 | 7.6 | 0.02862 | 12.8 | 0.000 | 0.772 | 0.004 |
| OTU28 | unident. Gammaproteobacteria | 2,147 | 0.235 | 0.00031 | 73.9 | 0.00008 | 47.6 | 0.00595 | 60.9 | 0.474 | 0.058 | 0.143 |
| OTU16 | Gilliamella apicola (97) | 7,951 | 0.225 | 0.00209 | 29.8 | 0.00033 | 47.9 | 0.02082 | 53.4 | 0.020 | 0.088 | 0.097 |
| OTU3 | Gilliamella apicola (99) | 203,595 | 0.222 | 0.26670 | 6.3 | 0.18932 | 14.2 | 0.20672 | 10.6 | 0.040 | 0.036 | 0.710 |
| OTU15 | Commensalibacter intestini (95) | 9,021 | 0.222 | 0.00318 | 25.7 | 0.00313 | 37.6 | 0.02174 | 65.8 | 0.975 | 0.011 | 0.241 |
| OTU25 | Lactobacillus melliventris (97) | 10,699 | 0.205 | 0.01301 | 12.4 | 0.02103 | 12.7 | 0.00863 | 13.4 | 0.031 | 0.024 | 0.001 |
| OTU18 | Frischella perrara (99) | 26,368 | 0.201 | 0.02100 | 12.8 | 0.01231 | 14.1 | 0.04773 | 19.9 | 0.021 | 0.005 | 0.002 |
| OTU33 | Bifidobacterium asteroides (98) | 18,563 | 0.200 | 0.02090 | 12.4 | 0.02553 | 14.9 | 0.02056 | 25.5 | 0.391 | 0.956 | 0.564 |
| OTU13 | Lactobacillus mellifer (99) | 8,712 | 0.198 | 0.00849 | 11.2 | 0.00991 | 18.8 | 0.01197 | 16.4 | 0.634 | 0.122 | 0.569 |
| OTU2 | Bartonella apis (99) | 77,679 | 0.197 | 0.05323 | 34.1 | 0.05017 | 46.4 | 0.14713 | 17.3 | 0.942 | 0.005 | 0.015 |
| OTU14 | Bifidobacterium asteroides (99) | 22,375 | 0.193 | 0.02504 | 11.0 | 0.04562 | 32.0 | 0.02027 | 21.1 | 0.219 | 0.354 | 0.133 |
| OTU10 | Enterococcus faecalis (99) | 16,167 | 0.193 | 0.03665 | 54.9 | 0.00029 | 19.6 | 0.00153 | 13.4 | 0.107 | 0.240 | 0.000 |
| OTU17 | Bifidobacterium coryneforme (99) | 7,768 | 0.189 | 0.00969 | 17.4 | 0.00523 | 17.2 | 0.00913 | 22.5 | 0.045 | 0.839 | 0.121 |
| OTU23 | Flavobacteriales | 2,974 | 0.183 | 0.00290 | 36.0 | 0.00294 | 26.3 | 0.00422 | 33.1 | 0.978 | 0.461 | 0.545 |
| OTU55 | Gilliamella apicola (98) | 38,619 | 0.176 | 0.04133 | 7.1 | 0.03045 | 8.1 | 0.05264 | 21.1 | 0.017 | 0.356 | 0.078 |
| OTU21 | Dysgonomonas | 3,944 | 0.173 | 0.00231 | 43.2 | 0.00541 | 37.8 | 0.00706 | 56.9 | 0.228 | 0.318 | 0.791 |
| OTU1 | Lactobacillus apis (99) | 131,977 | 0.163 | 0.13239 | 11.0 | 0.15581 | 12.7 | 0.17471 | 14.8 | 0.486 | 0.162 | 0.670 |
Notes.
aOTU, number of sequences in a standardized database; the detailed description of the OTUs is given in the raw dataset provided in Table S2.