## 2 Materials and Methods
### Monitoring of Bacterial Growth  
The concentrations of cells were determined in samples taken during mono- and co-culture by:  
(i)Plate count determination  
Viable (cultivable) _Lactobacillus_ or yeast counts were determined by spread-plating 10-fold serial dilutions (in 0.1%, _w/v_, sterilized peptone water) on MRS agar (de Mann, Rogosa and Sharpe agar is selective for _Lactobacillus_ due to lack of lactose consumption by yeast) or on YEPAL agar (selective for _S. cerevisiae_ due to lack of consumption of lactic acid by _Lactobacillus_), and incubated aerobically at 37 \({}^{\circ}\)C and 30 \({}^{\circ}\)C for 48 h for lactic acid bacteria strains and the yeast, respectively. The viable (cultivable) counts were expressed as the number of colony-forming units (CFU) per mL. (ii)qPCR (total cells) and PMA-qPCR (viable cells) analysis  
To distinguish viable from dead cells of _L. rhamnus_, qPCR in combination with propidium monoazide (PMA) (PMA-qPCR) was used to determine the log of total cells (qPCR) or viable cells per mL (PMA-qPCR). As PMA is cell membrane-impermeable, it only covalently binds, after photoactivation, to double-stranded DNA of damaged cells and will inhibit DNA amplification during qPCR [27, 28]. Samples taken were immediately diluted 1:10 with peptone water (1 g/L BactoPeptone and 0.5 g/L NaCl). For the PMA-qPCR analyses, the diluted samples were treated with 50 \(\upmu\)M PMA (Biotin, Hayward, CA, USA) and incubated in the dark at room temperature for 5 min while gently being shaken. Next, the PMA-treated cell suspensions were placed in an LED-Active Blue system (Ingenia Bio- systems, Barcelona, Spain) for 15 min and centrifuged at 15,000\(\times\)_g_ for 20 min at 4 \({}^{\circ}\)C. Samples not treated with PMA were centrifuged immediately after dilution at 15,000\(\times\)_g_ for 20 min at 4 \({}^{\circ}\)C. Cell pellets were stored at -80 \({}^{\circ}\)C until DNA extraction. Genomic DNA (gDNA) was extracted using the DNEasy Blood and Tissue kit (Qiagen, Mississauga, ON, Canada) with minor modifications of the manufacturer's protocol for Gram-positive bacteria (Qiagen): 2.5 \(\upmu\)L/mL mutanolysin (20 U/mL; Sigma-Aldrich) was added to the lysis buffer and an additional incubation with DNase-free RNase (Roche, Laval, QC, Canada) was performed at 37 \({}^{\circ}\)C for 60 min according to the manufacturer's instructions. The extracted gDNA was stored at -20 \({}^{\circ}\)C until qPCR amplification. Primers for qPCR targeting the _tuf_ gene in _L. rhamn_s (Table S1 in the supplemental material) were designed with Geneious Pro 5.3 (Biomatters, Auckland, New Zealand) on the basis of the complete genome sequence of _L. rhamn_s R0011 and the EPS gene cluster of the strains of _L. rhamn_s R0011, ATCC9595, and RW-9595M (National Center for Biotechnology Information [NCBI; NCBI Resource Coordinators, 2015] database accession numbers NZ_AGKC00000000 and AY659978.1; AY659976.1; AY659979.1, respectively). With the same software, the presence of hairpins, self-dimers, and pair-dimers was checked. The primers were synthesized by Integrated DNA Technologies (Coralville, IA, USA). Gene- and strain-specificity of the primers was confirmed in silico by Primer-Blast and by qPCR analysis on gDNA of both strains (the cycle threshold value [Ct] was undetermined for _S. cerevisiae_ (Table S1 due to lack of amplification) [29]. qPCR was performed using a 7500 Fast Real-Time PCR system (Applied Biosystems, Carlsbad, CA, USA) with 96-well plates. Each PCR reaction mixture of 20 \(\upmu\)L contained 10 \(\upmu\)L of Fast SYBR Green Master Mix (Life Technologies, Burlington, ON, Canada), 1 \(\upmu\)L of the extracted gDNA, 1 \(\upmu\)L of each primer at their optimal concentrations (Table S1), and 8 \(\upmu\)L of sterile nuclease-free water (Qiagen).