Table 2.
Frequency of rDNA motifs significantly enriched in the gut microbiota from gastrectomised (A) or sham-operated (B) GK rats
| Motif | Sham | VSG | p value | Sequence homology with bacteria | Accession | |
|---|---|---|---|---|---|---|
| A (%) | V13A7759 | 9.074 ± 3.114 | 22.706 ± 5.539 | 0.046 | Prevotella copri DSM 18205 | NZ_GG703862 |
| V13A9309 | 0.350 ± 0.243 | 1.017 ± 0.228 | 0.015 | – | – | |
| V13A14410 | 0.003 ± 0.002 | 0.636 ± 0.548 | 0.002 | – | – | |
| V13A14225 | 0.064 ± 0.047 | 0.310 ± 0.097 | 0.020 | – | – | |
| V13A12206 | 0.142 ± 0.116 | 0.206 ± 0.053 | 0.036 | – | – | |
| V13A1861 | 0.031 ± 0.008 | 0.124 ± 0.024 | 0.002 | Mannheimia haemolytica M42548 | NC_021082 | |
| Mannheimia succiniciproducens MBEL55E | NC_006300 | |||||
| Necropsobacter massiliensis strain FF6 | NZ_CDON01000005 | |||||
| Pasteurella bettyae CCUG 2042 | NZ_AJSX01000044 | |||||
| Rodentibacter heylii strain 1,998,236,014 | NZ_MLAA01000050 | |||||
| V13A11382 | 0.010 ± 0.010 | 0.088 ± 0.039 | 0.014 | – | – | |
| V13A9569 | 0.012 ± 0.003 | 0.035 ± 0.007 | 0.008 | Anaerotignum lactatifermentans DSM 14214 | NZ_FRAH01000002 | |
| V13A12536 | 0.001 ± 0.001 | 0.020 ± 0.008 | 0.018 | Planococcus halocryophilus Or1 | NZ_CP016537 | |
| V13A7019 | Absent | 0.008 ± 0.004 | 0.020 | – | – | |
| B (%) | V13A6709 | 3.043 ± 0.538 | 1.494 ± 0.237 | 0.046 | Prevotella pleuritidis JCM 14110 | NZ_BAJN01000030 |
| V13A8451 | 1.814 ± 0.615 | 0.096 ± 0.040 | 0.008 | – | – | |
| V13A399 | 0.902 ± 0.117 | 0.484 ± 0.167 | 0.011 | Planktothrix agardhii NIVA-CYA 126/8 | NZ_CM002803 | |
| V13A10048 | 0.665 ± 0.266 | 0.004 ± 0.003 | 0.033 | – | – | |
| V13A12857 | 0.286 ± 0.141 | 0.023 ± 0.006 | 0.014 | Eubacterium eligens ATCC 27750 | NC_012778 | |
| Eubacterium hallii DSM 3353 | NZ_ACEP01000116 | |||||
| Eubacterium ramulus ATCC 29099 | NZ_KI271105 | |||||
| Lactobacillus rogosae strain ATCC 27753 | NZ_FONU01000001 | |||||
| V13A9832 | 0.273 ± 0.097 | Absent | 0.021 | – | – | |
| V13A234 | 0.148 ± 0.031 | 0.071 ± 0.058 | 0.019 | Bacteroides paurosaccharolyticus JCM 15092 | NZ_BAJR01000054 | |
| V13A686 | 0.137 ± 0.052 | 0.022 ± 0.011 | 0.036 | – | – | |
| V13A603 | 0.136 ± 0.057 | 0.018 ± 0.018 | 0.037 | – | – | |
| V13A7033 | 0.130 ± 0.019 | 0.065 ± 0.009 | 0.011 | – | – | |
| V13A622 | 0.075 ± 0.036 | 0.015 ± 0.005 | 0.048 | Ruminococcus flavefaciens MC2020 | NZ_JNKE01000007 | |
| V13A1295 | 0.073 ± 0.015 | 0.035 ± 0.011 | 0.046 | – | – | |
| V13A6720 | 0.032 ± 0.013 | 0.005 ± 0.003 | 0.019 | – | – | |
| V13A1442 | 0.024 ± 0.006 | 0.001 ± 0.001 | 0.002 | – | – | |
| V13A6490 | 0.018 ± 0.007 | 0.004 ± 0.002 | 0.012 | – | – | |
| V13A12243 | 0.011 ± 0.004 | 0.002 ± 0.001 | 0.025 | – | – |
Data are shown as means of motif frequency ± SEM
Sequences of the rDNA motifs are given in ESM Table 2, along with data from the set of rDNA motifs present in caecum samples in at least 50% of individual rats at a frequency >0.005%. Only known bacteria showing full sequence homology with rDNA motifs are given