Table I.
Phylogenetic affiliation of 95 bacterial isolates and 16 yeast isolates from complex consortium TR15 cultivated on cheeses.
| Agar plate medium origin | RFLP clusters1 | Number of isolates | Species-specific PCR amplifications2 | Number of sequenced isolates | Closest 16S and 26S rDNA sequences > 99% homology | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| (a) Bacteria | |||||||||||
| paracasei | Lpl | Lc | Lmn1 | Lncit1 | ddlE1 | ddlF1 | Gram+ Catalase− | ||||
| FH and CRBM | G1 | 16 | + | − | − | − | − | − | − | 2 | 2 Lactobacillus casei |
| − | − | + | − | − | − | − | 2 | 2 Lactobacillus curvatus | |||
| MSE, FH and CRBM (days 11, 18, 21 and 28) | G2 | 12 | − | − | − | + | − | − | − | 3 | Leuconostoc pseudomesenteroides |
| SB and CRBM (days 21 and 28) | G3 | 11 | − | − | − | − | − | + | − | 1 | Enterococcus faecalis |
| CRBM (days 21 and 28) | G4 | 2 | − | − | − | − | − | − | − | 2 | Carnobacterium mobile |
| CRBM (days 21 and 28) | G5 | 5 | − | − | − | − | − | − | − | 5 | Marinilactibacillus psychrotolerans |
| Gram+ Catalase+ | |||||||||||
| CRBM (days 21 and 28) | G6 | 13 | 7 | 1 Arthrobacter nicotianae – arilaitensis | |||||||
| 6 Arthrobacter ardleyensis – bergerei | |||||||||||
| CRBM (days 21 and 28) | G7 | 4 | 3 | 2 Brevibacterium linens – casei | |||||||
| 1 Brevibacterium casei – antiquum (97% homology) | |||||||||||
| CRBM (days 21 and 28) | G8 | 1 | 1 | Brachybacterium sp. | |||||||
| CRBM and RPF (days 18, 21 and 28) | G10 | 4 | 4 | 3 Staphylococcus pulvereri | |||||||
| 1 Staphylococcus xylosus | |||||||||||
| Gram− | |||||||||||
| PCA + M + CV, CFC and RPF (days 18, 21 and 28) | G11 | 17 | 3 | Pseudomonas fluorescens – syringae | |||||||
| PCA + M + CV (day 18) | G12 | 2 | 2 | Serratia proteomaculans – liquefaciens | |||||||
| RPF (days 18 and 21) | G9 | 8 | 4 | Proteus vulgaris | |||||||
| (b) Yeasts | |||||||||||
| Physiological identification 3 | |||||||||||
| OGA (day 18) | 11 | Candida sake/tropicalis | 2 | Candida sake | |||||||
| OGA (day 18) | 2 | Yarrowia lipolytica | 2 | Yarrowia lipolytica | |||||||
| OGA (day 18) | 3 | Debaryomyces hansenii | 3 | Debaryomyces hansenii | |||||||
| Total number of isolates | 111 | 46 | |||||||||
(a) Bacteria: 16S rRNA gene analysis by the RFLP method followed by 16S rRNA gene sequencing, (b) Yeasts: phenotypic identification and 26S rRNA gene sequencing. In brackets () are indicated the time of ripening where the isolate was found. Media details in Section 2.4.
RFLP patterns were analysed with BioNumerics software using UPGMA analysis. Isolates with the same pattern were grouped together and one or several isolates from each group were analysed by 16S rDNA sequencing.
The description of primers is given in Table II.
Phenotypic identification using the morphological, biochemical and physiological characteristics and assignment to species as described by Callon et al. [7].