TABLE 3.
Combination of distance-based and sequence-based data with the analysis of signature proteins for each phylogroup
| Phylogroup | No. of species | AAI (%)g | POCPg | Presence of the following gene: |
||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| pfk | QTS_569 | QTS_898 | QTS_1754 | QTS_2490 | QTS_2425 | QTS_2525 | QTS_3870 | QTS_4397 | QTS_4707 | QTS_494 | QTS_497 | QTS_502 | QTS_509 | QTS_514 | QTS_898 | QTS_2490 | ||||
| L. delbrueckii | 35 | 52.1 (59.3a) | 46.4 (52.9a) | + | − | − | − | + | + | + | − | − | − | |||||||
| L. alimentarius | 21 | 52.8 (68.4b) | 44.6 (62.4b) | + | + | + | − | − | − | + | − | − | + | |||||||
| L. perolens | 4 | 55.9 (72.9c) | 48 (67.8c) | + | + | + | − | − | − | + | − | − | + | |||||||
| L. casei | 16 | 59.3 | 55.2 | + | + | + | − | − | − | − | + | + | − | |||||||
| L. sakei | 4 | 76.7 | 75.2 | + | + | + | − | − | − | − | − | − | − | |||||||
| L. plantarum | 9 | 76.5 | 76 | + | + | + | + | − | − | + | − | − | − | |||||||
| L. coryniformis | 5 | 62.5 | 61.1 | + | + | + | + | − | − | − | + | + | − | |||||||
| L. salivarius | 27 | 56.1 (61.1d) | 53.5 (59.3d) | + | + | + | + | − | − | − | − | − | − | |||||||
| L. concavus- L. dextrinicus | 2 | 72.7 | 70.9 | + | + | + | − | − | − | − | − | − | − | |||||||
| L. selangorensis | 1 | + | + | + | − | + | − | − | + | + | − | |||||||||
| L. reuteri | 23 | 63.2 (57.6e) | 62 (51e) | − | + | + | + | + | + | − | − | |||||||||
| L. vaccinostercus | 68.9 | 69 | − | + | + | + | + | + | − | − | ||||||||||
| L. fructivorans | 48 | 58.3 (56.1f) | 58.3 (45.9f) | − | + | + | + | + | + | + | − | |||||||||
| L. brevis | 74.6 | 70.8 | − | + | + | + | + | + | + | + | ||||||||||
| L. buchneri | 63.3 | 55.6 | − | + | + | + | + | + | + | − | ||||||||||
| L. collinoides | 62.07 | 62.2 | − | + | + | + | + | + | + | − | ||||||||||
| L. rossiae- L. siliginis | 2 | 73.7 | 67.3 | − | + | + | + | + | + | − | − | |||||||||
AAI and POCP values for the L. delbrueckii group without considering peripheral species (L. amylophilus, L. amylotrophicus, L. floricola).
AAI and POCP values for the L. alimentarius group without considering peripheral species (Lactobacillus mellifer, Lactobacillus mellis).
AAI and POCP values for the L. perolens group without considering peripheral species (Lactobacillus composti).
AAI and POCP values for the L. salivarius group without considering peripheral species (Lactobacillus algidus).
AAI and POCP values considering members of the L. reuteri and L. vaccinostercus groups.
AAI and POCP values considering members of the L. fructivorans, L. brevis, L. buchneri, and L. collinoides groups.
Numbers in bold are values of >55 to 60% ANI and >50% POCP, which are the thresholds empirically taken as genus delineation. Lower percentages are found within a single phylogroup.