Table 1. ITS restriction fingerprinting and direct sequencing of ITS regions and 26S rDNA D1/D2 domains.
Clusters G-1 to G-9 and singleton ITS profiles (-) are determined based on restriction digestion patterns of ITS amplicons with the endonucleases HaeIII, HhaI and HinfI. Restriction fragments lower than 70 bp are omitted from the analysis. Strains in bold are chosen as representatives of each cluster and/or unique ITS genotypes and are submitted to direct ITS and D1/D2 sequencing. Overlapping peaks in chromatograms due to ambiguous sites and/or indels are indicated as unreadable sequences. Closest-sequence matches are reported together with identity (%). Abbreviations: na, not applicable; nd, not determined; cp, copy.
| Source | Strains | Amp (bp) | ITS PCR-RFLP | Group | Closest Blast hits (Accession number; identity %) | |||
|---|---|---|---|---|---|---|---|---|
| HaeIII | HinfI | HhaI | ITS | 26S D1/D2 | ||||
| Honey | ||||||||
| 2,3, 12, 24, 56, 68, 76 | 900 | 570-200-80 | 380-280-180 | 300-220-190-100 | G-1 | Z. mellis type α (AY046190;100) | Z. mellis (U72164;99) | |
| 4, 7, 23, 35, 40, 1CF, 6C | 900 | 680–170 | 480-290-140 | 310-190-100 | G-2 | Z. mellis type β (AB302839;99) | Z. mellis (AB302835;100) | |
| 9, 27, 41 | 900 | 390-250-170 | 480-290-140 | 300-190-100 | G-3 | nd | Z. mellis (U72164;99) | |
| 70 | 900 | 680–170 | 480-290-140 | 380-320-130 | - | no significant entries | Z. mellis (U72164;99) | |
| 5CF | 700 | 700 | 360-270-250-220-180 | 360-290-200-170-100 | - | D. hansenii (EF192224;100) | D. hansenii (KF273863;100) | |
| Traditional Balsamic Vinegar | ||||||||
| B8911, B8932, B8933, B8941, B89221 | 700 | 390-210-90 | 360-250-180 | 290-200-170-100 | G-4 | Z. rouxii (AM943655;99) | Z. rouxii (AM943655; 100) | |
| B8943 | 650 | 420–150 | 450–280 | 300–290 | G-5 | Z. bailii (JX458100;100) | Z. bailii (AY046191; 99) | |
| M21, M22, M23, M25 | 700 | 510-480-390-250-210-170-90 | 380-360-260-250-220-180 | 360-290-200-170-100 | G-6 | unreadable sequence | Z. sapae (AJ966342;100) | |
| Shoyu mash, Shoyu moromi, and Miso | ||||||||
| NBRC 0495 | 700 | 480-440-220-170 | 360-250-220-110 | 320-290-200-170-100 | - | unreadable sequence | unreadable sequence | |
| NBRC 0505, NBRC 0506, NBRC 0521, NBRC 0523 | 700 | 480-170-90 | 360-160-130 | 320-290-100 | G-7 | Z. sapae cp 2 (AM2794964;99) | unreadable sequence | |
| NBRC 0525 | 700 | 480-170-90 | 340-220-190 | 320-290-100 | - | Z. sapae cp 2 (AM2794964;99) | unreadable sequence | |
| NBRC 0845, NBRC 0846 | 700 | 390-210-90 | 360-250-180 | 290-200-170-100 | G-4 | Z. rouxii (AM943655;99) | Z. sapae (AJ966342; 100) | |
| NBRC 10652, NBRC 10655 | 700 | 390-210-170-90 | 360-250-220-180 | 320-290-200-170-100 | G-8 | unreadable sequence | unreadable sequence | |
| NBRC 10668 | 700 | 390-170-90 | 360-250-220-180 | 320-290-100 | - | CBS 4837 cp 2 (HE664090;99) | Z. sapae (AJ966342;100) | |
| NBRC 10669 | 700 | 480-390-210-90 | 360-280-250-220-180 | 290-200-170-100 | - | unreadable sequence | unreadable sequence | |
| NBRC 10670 | 700 | 480-390-210-90 | 360-250-180 | 290-200-170-100 | - | unreadable sequence | unreadable sequence | |
| NBRC 10672 | 700 | 480-390-250-210-170-90 | 360-250-220-150 | 290-200-170-100 | - | unreadable sequence | unreadable sequence | |
| Reference strains | ||||||||
| Z. bailii CBS 680T | 650 | 420–150 | 450–280 | 300–290 | G-5 | na | na | |
| Z. mellis CBS 736T | 900 | 570-200-80 | 380-280-180 | 300-220-190-100 | G-1 | na | na | |
| Z. rouxii CBS 732T | 700 | 390-210-90 | 360-250-180 | 290-200-170-100 | G-4 | na | na | |
| Z. sapae ABT301T, ABT601 | 700 | 510-480-390-250-210-170-90 | 380-360-260-250-220-180 | 360-290-200-170-100 | G-6 | unreadable sequence | na | |
| Z. pseudorouxii NCYC 3042 | 700 | 480-170-90 | 360-220-180 | 320-290-100 | - | Z. sapae cp 2 (AM2794964;99) | Z. sapae (AJ966342;100) | |
| Allodiploid lineage ATCC 42981, CBS 4837, CBS 4838 | 700 | 480-390-250-210-170-90 | 380-360-250-230-180 | 360-290-200-170-100 | G-9 | unreadable sequence | unreadable sequence | |