| Xanthobacter autotrophicus | NBRC 14758, NBRC 102463T |
| Xanthobacter flavus | NBRC 14759T |
| Xanthobacter sp. | NBRC 15493, NBRC 15494, NBRC 115927, NBRC 116939, NBRC 116940 |
| Xanthomonas arboricola | NBRC 3780, NBRC 13557 |
| Xanthomonas campestris | NBRC 13303, NBRC 13551 |
| Xanthomonas citri | NBRC 3781, NBRC 3829, NBRC 3835, NBRC 12213 |
| Xanthomonas cucurbitae | NBRC 13552 |
| Xanthomonas oryzae | NBRC 3312, NBRC 3510, NBRC 3827, NBRC 3828, NBRC 3833, NBRC 3834, NBRC 3995, NBRC 3996, NBRC 3997, NBRC 3998, NBRC 3999, NBRC 12000, NBRC 12001, NBRC 12002 |
| Xanthomonas phaseoli | NBRC 13553, NBRC 13554 |
| Xanthomonas physalidicola | NBRC 13555 |
| Xanthomonas pisi | NBRC 13556 |
| Xanthomonas sp. | NBRC 14591, NBRC 115641 |
| Xanthomonas translucens | NBRC 13559 |
| Xanthophyllomyces dendrorhous | NBRC 10129, NBRC 10130 |
| Xanthothecium peruvianum | NBRC 8500, NBRC 9865 |
| Xenobotrytis acaducospora | NBRC 102034 |
| Xeromphalina cauticinalis | NBRC 7633, NBRC 9358 |
| Xeromyces bisporus | NBRC 112787 |
| Xerula pudens | NBRC 9574, NBRC 30335 |
| Xylanibacterium ulmi | NBRC 106152T |
| Xylanimicrobium pachnodae | NBRC 107786T |
| Xylanimonas allomyrinae | NBRC 113052T |
| Xylanimonas cellulosilytica | NBRC 107835T |
| Xylanimonas protaetiae | NBRC 113053T |
| Xylaria angulosa | NBRC 33288 |
| Xylaria aristata | NBRC 104662, NBRC 104667 |
| Xylaria badia | NBRC 104656, NBRC 104660 |
| Xylaria berteroi | NBRC 112119 |
| Xylaria carpophila | NBRC 33013 |
| Xylaria cf. amphithele | NBRC 104702 |
| Xylaria cubensis | NBRC 104653, NBRC 104655, NBRC 104661, NBRC 104669, NBRC 104681, NBRC 104693, NBRC 104722, NBRC 104724, NBRC 107985, NBRC 107986, NBRC 107987, NBRC 107988, NBRC 107991, NBRC 107992, NBRC 107994, NBRC 107995, NBRC 107996, NBRC 107997, NBRC 107998, NBRC 107999, NBRC 108000, NBRC 108007, NBRC 108008 |
| Xylaria escharoidea | NBRC 104735, NBRC 104736 |
| Xylaria grammica | NBRC 104680, NBRC 104688, NBRC 104697, NBRC 104709, NBRC 104711, NBRC 104721, NBRC 104727, NBRC 104730, NBRC 104731, NBRC 104732, NBRC 107983, NBRC 107984, NBRC 107989 |
| Xylaria juruensis | NBRC 104663, NBRC 104664, NBRC 104665 |
| Xylaria laevis | NBRC 104659 |
| Xylaria polymorpha | NBRC 9780, NBRC 30369 |
| Xylaria sp. | NBRC 104428, NBRC 104429, NBRC 104430, NBRC 104431, NBRC 104432, NBRC 104658, NBRC 104668, NBRC 104671, NBRC 104672, NBRC 104673, NBRC 104674, NBRC 104676, NBRC 104677, NBRC 104678, NBRC 104679, NBRC 104682, NBRC 104683, NBRC 104684, NBRC 104685, NBRC 104687, NBRC 104690, NBRC 104691, NBRC 104694, NBRC 104695, NBRC 104705, NBRC 104706, NBRC 104707, NBRC 104708, NBRC 104710, NBRC 104715, NBRC 104718, NBRC 104719, NBRC 104720, NBRC 104729, NBRC 104996, NBRC 107815, NBRC 107824, NBRC 112117 |
| Xylariaceae sp. | NBRC 113725, NBRC 113728, NBRC 113731, NBRC 113732, NBRC 113733 |
| Xylobolus frustulatus | NBRC 4932 |
| Xylobolus spectabilis | NBRC 7650 |
| Xylobolus subpileatus | NBRC 7076 |
| Xylogone sphaerospora | NBRC 9516T, NBRC 31724 |
| Xylomyces sp. | NBRC 105263 |
