Brewer's Spent Grain Enhanced the Recovery of Potential Probiotic Strains in Fermented Milk After Exposure to In Vitro-Simulated Gastrointestinal Conditions.

Brewer's spent grain (BSG) is a beer industry by-product with interesting functional properties by its high fiber content and bioactive compounds, which may be possibly employed as a prebiotic ingredient. The fermentability of BSG by ten probiotics and two starter cultures was evaluated, and the co-culture of Lacticaseibacillus paracasei subsp. paracasei F-19® (probiotic) and Streptococcus thermophilus TH-4® (starter) was selected to produce a potentially probiotic fermented milk (FM). Four formulations of FM were studied: FM1 (control), FM2 (probiotic - /BSG +), FM3 (probiotic + /BSG -), and FM4 (probiotic + /BSG +). The viability of the microorganisms in the FM was monitored throughout 28 days of storage. The resistance of the microorganisms in the FM to in vitro-simulated gastrointestinal tract (GIT) conditions was also evaluated. Even though the BSG did not influence the fermentation kinetics or increase the populations of both microorganisms in the FM, a significant improvement on the survival of TH-4® against in vitro-simulated GIT stress was observed in the formulations containing BSG alone or in combination with F-19®. All formulations showed potential as probiotic FM, since total probiotic populations were kept above 1010 CFU in a daily portion of 200 mL, and a minimum of 1010 and 108 CFU equivalent of, respectively, TH-4® and F-19® was recovered after the GIT stress. Therefore, TH-4® has potential as a probiotic strain in addition to its starter feature, while BSG may be employed as a possible prebiotic ingredient in a synbiotic approach. Nonetheless, further studies to evaluate possible health benefits are needed.

Impact of a fermented soy beverage supplemented with acerola by-product on the gut microbiota from lean and obese subjects using an in vitro model of the human colon.

The aim of this study was to evaluate the effects of soy-based beverages manufactured with water-soluble soy extract, containing probiotic strains (Lactobacillus acidophilus LA-5 and Bifidobacterium longum BB-46) and/or acerola by-product (ABP) on pooled faecal microbiota obtained from lean and obese donors. Four fermented soy beverages (FSs) ("placebo" (FS-Pla), probiotic (FS-Pro), prebiotic (FS-Pre), and synbiotic (FS-Syn)) were subjected to in vitro digestion, followed by inoculation in the TIM-2 system, a dynamic in vitro model that mimics the conditions of the human colon. Short- and branched-chain fatty acids (SCFA and BCFA) and microbiota composition were determined. Upon colonic fermentation in the presence of the different FSs formulations, acetic and lactic acid production was higher than the control treatment for faecal microbiota from lean individuals (FMLI). Additionally, SCFA production by the FMLI was higher than for the faecal microbiota from obese individuals (FMOI). Bifidobacterium spp. and Lactobacillus spp. populations increased during simulated colonic fermentation in the presence of FS-Syn in the FMLI and FMOI. FS formulations also changed the composition of the FMOI, resulting in a profile more similar to the FMLI. The changes in the composition and the increase in SCFA production observed for the FMLI and FMOI during these in vitro fermentations suggest a potential modulation effect of these microbiotas by the consumption of functional FSs. KEY POINTS: • Soy beverages increased Bifidobacterium abundance in microbiota from obese individuals. • The synbiotic beverage increased Bifidobacterium abundance in microbiota from lean individuals. • The synbiotic beverage changed the microbiota from obese individuals, approaching the lean profiles.

Impact of Acerola (Malpighia emarginata DC) Byproduct and Probiotic Strains on Technological and Sensory Features of Fermented Soy Beverages.

Ten probiotic cultures were screened for the ability to hydrolyze soy proteins and bile salt deconjugation (BSD) to select one lactobacilli and one bifidobacteria strain to produce fermented soy beverages (FSBs) containing acerola byproduct (ABP). Next, the effect of the strains and the ABP on the technological and sensory characteristics of these beverages was evaluated during refrigerated storage for up to 28 days. None of the tested strains presented any proteolytic activity against soy proteins. Among the probiotic strains, the best BSD activities were observed for Lactobacillus acidophilus LA-5 and Bifidobacterium longum BB-46, which were further employed, individually or combined, to produce FSB supplemented or not with ABP, using Streptococcus thermophilus TH-4 as a starter, and the effect of these strains and ABP on the technological and sensory acceptability of FSB was evaluated. The probiotic strains did not influence FBS texture parameters, but ABP increased firmness in the ready product. BB-46 increased acidity, therefore decreasing acceptance, whereas the presence of LA-5 and/or ABP increased acceptance, even though the appearance was negatively affected by ABP after 21 days of storage. Thus, the presence of LA-5 and ABP contributed for the sensory acceptance of the FSBs without affecting their technological features. PRACTICAL APPLICATION: Lactobacillus acidophilus LA-5, Bifidobacterium longum BB-46, and/or acerola byproduct (ABP) were applied in the production of fermented soy beverages (FSBs). Principal components analysis was used to evaluate the formulations of the 23 factorial design and the sensory attributes and the effect of storage independently and covariance was the matrix type used for mapping purposes. LA-5 and ABP contributed for the sensory acceptance of FSB, without affecting their technological features, and could be used by food processing companies after scaling up, also reducing the environmental impact by decreasing discarding byproducts, which are sources of bioactive compounds.

Impact of the incorporation of probiotic strains and fruit by-products in fermented synbiotic soy product and on the composition and metabolic activity of the gut microbiota in vitro / Impacto da incorporação de cepas probióticas e de subprodutos de frutas em um produto fermentado de soja simbiótico e sobre a composição e a atividade metabólica da microbiota intestinal humana in vitro

The present study aimed to develop a fermented soy beverage containing fruit by-products and probiotics and to evaluate the impact of this product on the composition and metabolic activity of the human intestinal microbiota using an in vitro simulation model of the intestinal conditions (TIM-2). Therefore, the present study was divided into three stages. Stage I was based on obtaining, processing and physical-chemical, microbiological and functional characterization of fruit by-products (acerola, orange, mango, and passion fruit) and soybean (okara), as well as amaranth flour. Additionally, the ability to use these vegetable by-products and amaranth flour by probiotic and non-probiotic strains was evaluated. The results showed that the acerola byproduct presented the highest dietary fibre content (48.46 g/100 g) among the by-products tested, as well as amaranth flour. Orange and passion fruit by-products were the substrates that most promoted the growth of bacterial populations, including strains of Escherichia coli and Clostridium perfringens. On the other hand, the acerola by-product was the substrate that showed the highest selectivity for beneficial bacteria. Also, in this stage, ten probiotic strains (seven lactobacilli and three bifidobacteria) and three starter strains (Streptococcus thermophilus) were tested for their ability to deconjugate bile salts and for proteolytic activity against milk and soy proteins. The results showed that none of the tested strain showed proteolytic ability against milk and soybean proteins. In addition, the probiotic strains Lactobacillus acidophilus LA-5 and Bifidobacterium longum BB-46 deconjugated more types of bile acids tested, and the strains of S. thermophilus tested showed no ability to deconjugate bile salts. Next, the acerola by-product (ABP) and the probiotic strains LA-5 and BB-46 were selected to continue stage II of the study (development of a fermented soy beverage). For this purpose, a 23 factorial design was used, in a total of 8 trials with three replicates of each one, and the effects of the probiotic strains and the acerola by-product on the physical-chemical, microbiological, and sensory characteristics of these fermented soy beverages were evaluated. At the same time, probiotic viability and survival under in vitro gastrointestinal (GI) simulated conditions were evaluated in fermented soy beverage (FSB). The results showed that the presence of BB-46 and ABP affected the sensory acceptability of FSB negatively. ABP also led to significant differences in the texture profile of the FSB (P<0.05). Populations of probiotic strains ranged from 7.0 to 8.2 log CFU equivalent/mL during 28 days of refrigerated storage (4° C) of FBS, and the co-culture (LA-5+BB-46) and the ABP did not affect the viability of both microorganisms significantly (P> 0.05). However, ABP increased the survival of BB-46 under in vitro simulated GI conditions significantly. For stage III, a 22 experimental design was performed. To evaluate the impact of these FBS on the composition and metabolic activity of the intestinal microbiota of lean and obese humans, a validated in vitro model called TIM-2 was used, available at the Maastricht University (Venlo, The Netherlands), which simulates normal conditions of the lumen of the proximal colon, with all parameters controlled by a computer. Samples were collected from TIM-2 to quantify probiotic microorganisms (LA-5 and BB-46), Lactobacillus spp., Bifidobacterium spp., and total bacteria, using the quantitative PCR method (qPCR) and the intestinal microbiota profile was determined using an Illumina Mysec Next Generation Sequencing (NGS) method. Concentrations of shortchain fatty acids and branched-chain fatty acids and lactate produced by the different microbiotas during fermentation in TIM-2 were also determined. The results showed that the lean microbiota presented the high production of acetate and lactate than the microbiota of obese individuals. Significant reductions in Bifidobacterium populations in the lean microbiota were observed at 0 and 48 h of an assay for all experimental meals, except for the meal that had the probiotic combination (LA-5 and BB-46) and the ABP supplementation, which showed an increased total Bifidobacterium and Lactobacillus populations throughout the experimental period for both microbiotas tested. The FSB supplemented with ABP presented the best characteristics regarding the modulation of the obese microbiota, with an increase in Bifidobacterium spp. and Lactobacillus spp. Additionally, after 48 hours of intervention in TIM-2, the obese microbiota was apparently similar to the lean microbiota, showing a beneficial modulation of this microbiota. The results suggest that the fermented soy beverage supplemented with the acerola by-product and the probiotic strains may present beneficial health effects. However, clinical studies are required to complement and confirm the results observed in the in vitro assays

O presente trabalho visou desenvolver uma bebida fermentada de soja adicionada de resíduos de frutas e suplementada com cepas probióticas e avaliar o impacto desse produto sobre a composição e a atividade metabólica da microbiota intestinal humana, utilizando um modelo de simulação in vitro das condições intestinais (TIM-2). Para tanto, o presente trabalho foi dividido em três etapas. A etapa I foi baseada na obtenção, processamento e caracterização físico-química, microbiológica e funcional de subprodutos de frutas (acerola, laranja, manga e maracujá) e soja (okara), bem como da farinha de amaranto. Adicionalmente, a capacidade de utilização desses subprodutos vegetais e da farinha de amaranto por cepas probióticas e não probióticas foi avaliada. Os resultados mostraram que o subproduto de acerola apresentou o maior conteúdo de fibras alimentares totais (48,46 g/100 g) dentre os subprodutos testados, bem como a farinha de amaranto. Os subprodutos de laranja e maracujá foram os substratos que mais promoveram a multiplicação das populações bacterianas, incluindo das cepas de Escherichia coli e Clostridium perfringens. Por outro lado, o subproduto de acerola foi o substrato que apresentou a maior seletividade para bactérias benéficas. Ainda nessa etapa, dez cepas probióticas (sete lactobacilos e três bifidobacterias) e três cepas starter (Streptococcus thermophilus) foram testadas quanto à sua capacidade de desconjugação de sais biliares e atividade proteolítica frente às proteínas do leite e da soja. Os resultados revelaram que nenhuma cepa testada apresentou capacidade de proteólise das proteínas do leite e da soja. Adicionalmente, as cepas probióticas Lactobacillus acidophilus LA-5 e Bifidobacterium longum BB-46 desconjugaram a maior quantidade de ácidos biliares testados e as cepas de S. thermophilus testadas não apresentaram capacidade de desconjugação de sais biliares. Após a análise dos resultados da etapa I, o resíduo de acerola (ABP) e as cepas probióticas LA-5 e BB-46 foram selecionadas para dar continuidade à etapa II do estudo(desenvolvimento de uma bebida fermentada a base de soja). Para esse fim, foi utilizado um delineamento experimental do tipo fatorial 23, totalizando 8 ensaios com três repetições de cada, e foram avaliados os efeitos das cepas probióticas e do subproduto de acerola sobre as características físico-químicas, microbiológicas e sensoriais dessas bebidas fermentadas de soja. Paralelamente, foram realizadas análises da sobrevivência das cepas probióticas frente às condições gastrintestinais simuladas in vitro nas bebidas fermentadas de soja (FSB). Os resultados mostraram que a presença de BB-46 e ABP afetaram negativamente a aceitabilidade sensorial das FSB. O ABP também levou a diferenças significativas no perfil de textura das FSB (P<0,05). As populações das cepas probióticas nas diferentes formulações de FSB variaram de 7,0 a 8,2 log de UFC equivalente/mL durante os 28 dias de armazenamento (4 ºC) e a co-cultura (LA-5+BB-46) e o ABP não afetaram (P>0,05) a viabilidade de ambos os microrganismos. No entanto, ABP aumentou significativamente a sobrevivência de BB-46 frente às condições gastrintestinais sumuladas in vitro. Para a etapa III do presente estudo, um delineamento experimental fatorial 22 foi realizado. Para a avaliação do impacto dessas FSB sobre a composição e atividade metabólica da microbiota intestinal de humanos eutróficos e obesos, foi utilizado um modelo in vitro TIM-2 na Maastricht University (Venlo, Holanda), que simula as condições normais do lúmen do cólon proximal, com todos os parâmetros controlados por um computador. Amostras foram coletadas do TIM-2 para a quantificação dos microrganismos probióticos (LA-5 e BB-46), Lactobacillus spp., Bifidobacterium spp. e bactérias totais, utilizando o método de PCR quantitativo (qPCR), e o perfil da microbiota intestinal foi determinado utilizando Next-Generation Sequencing (NGS) Illumina Mysec. A concentração de ácidos graxos de cadeia curta e de cadeia ramificada e lactato produzidos pelas diferentes microbiotas durante a fermentação no TIM-2 também foi determinada. Os resultados mostraram que a microbiota de humanos eutróficos apresentou uma alta produção de acetato e lactato em comparação com a microbiota de obesos. Reduções significativas das populações de Bifidobacterium na microbiota de eutróficos foram observadas entre 0 e 48 h de ensaio para todas as refeições experimentais, exceto para a refeição que apresentou a combinação probiótica (LA-5 e BB-46) e a suplementação com ABP, que apresentou aumento de Bifidobacterium e Lactobacillus totais durante todo o período de análise para ambas as microbiotas testadas. As FSB suplementadas com ABP apresentaram os melhores resultados em relação à modulação da microbiota de humanos obesos, com o aumento Bifidobacterium spp. e Lactobacillus spp. Adicionalmente, após 48 horas de intervenção no TIM-2, a microbiota de obesos foi aparentemente similar à microbiota de eutróficos, mostrando uma modulação benéfica dessa microbiota. Os resultados sugerem que as bebidas fermentadas de soja suplementadas com o subproduto de acerola e cepas probióticas podem apresentar efeitos benéficos à saúde. No entanto, estudos clínicos são necessários para complementar e confirmar os resultados observados nos ensaios in vitro

The impact of fruit and soybean by-products and amaranth on the growth of probiotic and starter microorganisms.

The ability of different fruit by-products, okara, and amaranth flour, to support the growth of probiotic and non-probiotic strains was evaluated. The tests were conducted with three commercial starter cultures (Streptococcus thermophilus), ten probiotic strains (seven Lactobacillus spp. and three Bifidobacterium spp. strains), and two harmful bacteria representative of the intestinal microbiota (Escherichia coli and Clostridium perfringens). In vitro fermentability assays were performed using a modified MRS broth supplemented with different fruits (acerola, orange, passion fruit, and mango), and soy (okara) by-products or amaranth flour. Orange and passion-fruit by-products were the substrates that most promoted the growth of bacterial populations, including pathogenic strains. On the other hand, the acerola by-product was the substrate that showed the highest selectivity for beneficial bacteria, since the E. coli and Cl. perfringens populations were lower in the presence of this fruit by-product. Although the passion fruit by-product, okara, and amaranth stimulated the probiotic strains, the growth of the pathogenic strains studied was higher compared to other substrates. Different growth profiles were verified for each substrate when the different strains were compared. Although pure culture models do not reflect bacterial interaction in the host, this study reinforces the fact that the ability to metabolize different substrates is strain-dependent, and acerola, mango, and orange by-products are the substrates with the greatest potential to be used as prebiotic ingredients.

Synbiotic Amazonian palm berry (açai, Euterpe oleracea Mart.) ice cream improved Lactobacillus rhamnosus GG survival to simulated gastrointestinal stress.

The effect of açai pulp ice cream and of its supplementation with inulin (I), whey protein concentrate (WC), and/or whey protein isolate (WI) on the viability and resistance to simulated gastrointestinal stress of the probiotic Lactobacillus (Lb.) rhamnosus GG strain throughout storage at -18 °C for up to 112 days was evaluated and morphological changes during stress were monitored. Lb. rhamnosus GG viability was stable in all formulations for up to 112 days of storage, preserving populations around 9 log CFU g-1. Compared to the fresh culture, Lb. rhamnosus GG showed higher survival under simulated gastrointestinal conditions when incorporated into açai ice cream, indicating that the presence of the food matrix contributed to the microorganism survival. A reduction of at least 5 log cycles of Lb. rhamnosus GG was observed in all formulations after the gastrointestinal simulation in all storage periods assessed. The addition of I, WC, and/or WI did not show any significant effect on the probiotic survival under simulated gastrointestinal stress (p < 0.05). Compared to the fresh culture, fewer morphological changes were observed when the probiotic was added to ice cream. Thus, the açai pulp ice cream was shown to be a suitable matrix for Lb. rhamnosus GG, improving its survival under in vitro simulated gastrointestinal conditions.

Supplementation with fruit and okara soybean by-products and amaranth flour increases the folate production by starter and probiotic cultures.

The ability of two starter cultures (Streptococcus (S.) thermophilus ST-M6 and St. thermophilus TA-40) and eleven probiotic cultures (St. thermophilus TH-4, Lactobacillus (Lb.) acidophilus LA-5, Lb. fermentum PCC, Lb. reuteri RC-14, Lb. paracasei subsp. paracasei, Lb. casei 431, Lb. paracasei subsp. paracasei F19, Lb. rhamnosus GR-1, and Lb. rhamnosus LGG, Bifidobacterium (B.) animalis subsp. lactis BB-12, B. longum subsp. longum BB-46, and B. longum subsp. infantis BB-02) to produce folate in a modified MRS broth (mMRS) supplemented with different fruit (passion fruit, acerola, orange, and mango) and okara soybean by-products and amaranth flour was investigated. Initially, the folate content of each vegetable substrate was determined: passion fruit by-product showed the lowest folate content (8±2ng/mL) and okara the highest (457±22ng/mL). When the orange by-product and amaranth flour were added to mMRS, all strains were able to increase folate production after 24h of fermentation. B. longum subsp infantis BB-02 produced the highest concentrations (1223±116ng/mL) in amaranth flour. Okara was the substrate that had the lowest impact on the folate production by all strains evaluated. Lb. acidophilus LA-5 (297±36ng/mL) and B. animalis subsp. lactis BB-12 (237±23ng/mL) were also able to produce folate after growth in mMRS containing acerola and orange by-products, respectively. The results of this study demonstrate that folate production is not only strain-dependent but also influenced by the addition of different substrates in the growth media.

A prebiotic mixture improved Lactobacillus acidophilus and Bifidobacterium animalis gastrointestinal in vitro resistance in petit-suisse.

The survival of two probiotic strains -Lactobacillus acidophilus La-5 and Bifidobacterium animalis Bb-12 - incorporated into probiotic (PC) and into synbiotic (SC, with inulin + fructooligosaccharides, respectively, at 7.5 and at 2.5 g per 100 g) petit-suisse cheese was investigated in the beginning (day 1) and at the end (28 days) of storage at 4 °C when the food products were subjected to in vitro gastrointestinal simulated assays. Species-specific quantitative real time PCR (qPCR) combined with propidium monoazide (PMA-qPCR) was employed to quantify the strains. Initial La-5 and Bb-12 populations were always above 7 log CFU g(-1). The presence of the prebiotic ingredients in SC improved the Bb-12 and La-5 resistance after the 6 h assay, with higher populations in all the in vitro stages and throughout the storage period (p < 0.05), leading to equal or superior survival rates (SR) in SC of both probiotic strains, in the beginning as well as at the end of storage. The mean La-5 SR were 58% (PC) and 67% (SC), whereas the mean Bb-12 SR were 60% (PC) and 79% (SC). Our findings suggest that the addition of a prebiotic mixture in petit-suisse cheese was advantageous, since it improved both the Bb-12 and La-5 viability and tolerance under in vitro gastrointestinal simulated conditions, both in the fresh product and in the product refrigerated for 28 days.

Safety, beneficial and technological properties of Enterococcus faecium isolated from Brazilian cheeses.

This study aimed to characterize the safety and technological properties of Enterococcus faecium strains isolated from Brazilian Coalho cheeses. High levels of co-aggregation were observed between Enterococcus faecium strains EM485 and EM925 and both Escherichia coli and Clostridium perfringens . Both strains presented low levels of hydrophobicity. E. faecium EM485 and EM925 were both able to grow in the presence of 0.5% of the sodium salts of taurocholic acid (TC), taurodeoxycholic acid (TDC), glycocholic acid (GC), and glycodeoxycholic acid (GDC), although they showed the ability to deconjugate only GDC and TDC. Both strains showed good survival when exposed to conditions simulating the gastro intestinal tract (GIT). When tested for the presence of virulence genes, only tyrosine decarboxylase and vancomycin B generated positive PCR results.

Safety, beneficial and technological properties of Enterococcus faecium isolated from Brazilian cheeses

This study aimed to characterize the safety and technological properties of Enterococcus faecium strains isolated from Brazilian Coalho cheeses. High levels of co-aggregation were observed between Enterococcus faecium strains EM485 and EM925 and both Escherichia coli and Clostridium perfringens. Both strains presented low levels of hydrophobicity. E. faecium EM485 and EM925 were both able to grow in the presence of 0.5% of the sodium salts of taurocholic acid (TC), taurodeoxycholic acid (TDC), glycocholic acid (GC), and glycodeoxycholic acid (GDC), although they showed the ability to deconjugate only GDC and TDC. Both strains showed good survival when exposed to conditions simulating the gastro intestinal tract (GIT). When tested for the presence of virulence genes, only tyrosine decarboxylase and vancomycin B generated positive PCR results.

Bacteriocin production and inhibition of Listeria monocytogenes by Lactobacillus sakei subsp. sakei 2a in a potentially synbiotic cheese spread.

Survival, bacteriocin(s) production, and antilisterial effect of Lactobacillus sakei subsp. sakei 2a were evaluated in a potentially synbiotic cheese spread, throughout storage at 4 °C and 15 °C for up to 28 days, using culture-dependent (plate count) and culture-independent (qPCR) methods. Bacteriocin(s) production in the food product was monitored by phenotypic and molecular (RT-qPCR) techniques. Three cheese spread trials (T) containing the prebiotic fiber inulin were produced in duplicates and studied: T1 (control - without inoculation of lactic acid bacteria); T2 (inoculated with the non-bacteriocinogenic Lb. sakei ATCC 15521 strain), and T3 (inoculated with the bacteriocinogenic Lb. sakei 2a strain). The cheese spreads were challenged with Listeria monocytogenes serotypes 4b and 1/2a, individually added to the food product. The counts of Lb. sakei 2a in the cheese spread T3 remained high during storage and the growth of L. monocytogenes was inhibited at both temperatures, especially L. monocytogenes 4b in the food product kept at 15 °C due to the production of bacteriocins (up to 6,400 AU/mL). Expression of the genes sakP and sakQ encoding for bacteriocins production during the cheese spread storage was demonstrated. Lb. sakei 2a can be used for production of potentially synbiotic cheese spreads with increased safety.

Advantageous direct quantification of viable closely related probiotics in petit-suisse cheeses under in vitro gastrointestinal conditions by Propidium Monoazide--qPCR.

Species-specific Quantitative Real Time PCR (qPCR) alone and combined with the use of propidium monoazide (PMA) were used along with the plate count method to evaluate the survival of the probiotic strains Lactobacillus acidophilus La-5 and Bifidobacterium animalis subsp. lactis Bb-12, and the bacteriocinogenic and potentially probiotic strain Lactobacillus sakei subsp. sakei 2a in synbiotic (F1) and probiotic (F2) petit-suisse cheeses exposed throughout shelf-life to in vitro simulated gastrointestinal tract conditions. The three strains studied showed a reduction in their viability after the 6 h assay. Bb-12 displayed the highest survival capacity, above 72.6 and 74.6% of the initial populations, respectively, by plate count and PMA-qPCR, maintaining population levels in the range or above 6 log CFU/g. The prebiotic mix of inulin and FOS did not offer any additional protection for the strains against the simulated gastrointestinal environment. The microorganisms' populations were comparable among the three methods at the initial time of the assay, confirming the presence of mainly viable and culturable cells. However, with the intensification of the stress induced throughout the various stages of the in vitro test, the differences among the methods increased. The qPCR was not a reliable enumeration method for the quantification of intact bacterial populations, mixed with large numbers of injured and dead bacteria, as confirmed by the scanning electron microscopy results. Furthermore, bacteria plate counts were much lower (P<0.05) than with the PMA-qPCR method, suggesting the accumulation of stressed or dead microorganisms unable to form colonies. The use of PMA overcame the qPCR inability to differentiate between dead and alive cells. The combination of PMA and species-specific qPCR in this study allowed a quick and unequivocal way of enumeration of viable closely related species incorporated into probiotic and synbiotic petit-suisse cheeses and under stress conditions.