Understanding microbial dispersal is critical to understand the dynamics and evolution of microbial communities. However, microbial dispersal is difficult to study because of uncertainty about their vectors of migration. This applies to both microbial communities in natural and human-associated environments. Here, we studied microbial dispersal along the sourdoughs bread-making chain using a participatory research approach. Sourdough is a naturally fermented mixture of flour and water. It hosts a community of bacteria and yeasts whose origins are only partially known. We analysed the potential of wheat grains and flour to serve as an inoculum for sourdough microbial communities using 16S rDNA and ITS1 metabarcoding. First, in an experiment involving farmers, a miller and bakers, we followed the microbiota from grains to newly initiated and propagated sourdoughs. Second, we compared the microbiota of 46 sourdough samples collected everywhere in France, and of the flour used for their back-slopping. The core microbiota detected on the seeds, in the flour and in the sourdough was composed mainly of microbes known to be associated with plants and not living in sourdoughs. No sourdough yeast species were detected on grains and flours. Sourdough lactic acid bacteria were rarely found in flour. When they were, they did not have the same amplicon sequence variant (ASV) as found in the corresponding sourdough. However, the low sequencing depth for bacteria in flour did not allow us to draw definitive conclusion. Thus, our results showed that sourdough yeasts did not come from flour, and suggest that neither do sourdough LAB.

The aim of this study was to develop a rapid and accurate PMA-qPCR method to quantify viable Brochothrix thermosphacta in cold-smoked salmon. B. thermosphacta is one of the main food spoilage bacteria. Among seafood products, cold-smoked salmon is particularly impacted by B. thermosphacta spoilage. Specific and sensitive tools that detect and quantify this bacterium in food products are very useful. The culture method commonly used to quantify B. thermosphacta is time-consuming and can underestimate cells in a viable but not immediately culturable state. We designed a new PCR primer set from the single-copy rpoC gene. QPCR efficiency and specificity were compared with two other published primer sets targeting the rpoC and rpoB genes. The viability dyes PMA or PMAxx were combined with qPCR and compared with these primer sets on viable and dead B. thermosphacta cells in BHI broth and smoked salmon tissue homogenate (SSTH). The three primer sets displayed similar specificity and efficiency. The efficiency of new designed rpoC qPCR on viable B. thermosphacta cells in SSTH was 103.50%, with a linear determination coefficient (r 2 ) of 0.998 and a limit of detection of 4.04 log CFU/g. Using the three primer sets on viable cells, no significant difference was observed between cells treated or untreated with PMA or PMAxx. When dead cells were used, both viability dyes suppressed DNA amplification. Nevertheless, our results did not highlight any difference between PMAxx and PMA in their efficiency to discriminate viable from unviable B. thermosphacta cells in cold-smoked salmon. Thus, this study presents a rapid, specific and efficient rpoC -PMA-qPCR method validated in cold-smoked salmon to quantify viable B. thermosphacta in foods.

Cold-smoked salmon is a widely consumed ready-to-eat seafood product that is a fragile commodity with a long shelf-life. The microbial ecology of cold-smoked salmon during its shelf-life is well known. However, to our knowledge, no study on the microbial ecology of cold-smoked salmon using next-generation sequencing has yet been undertaken. In this study, cold-smoked salmon microbiotas were investigated using a polyphasic approach composed of cultivable methods, V3—V4 16S rRNA gene metabarcoding and chemical analyses. Forty-five cold-smoked salmon products processed in three different factories were analyzed. The metabarcoding approach highlighted 12 dominant genera previously reported as fish spoilers: Firmicutes Staphylococcus, Carnobacterium, Lactobacillus, β-Proteobacteria Photobacterium, Vibrio, Aliivibrio, Salinivibrio, Enterobacteriaceae Serratia,Pantoea, γ-Proteobacteria Psychrobacter, Shewanella and Pseudomonas. Specific operational taxonomic units were identified during the 28-day storage study period. Operational taxonomic units specific to the processing environment were also identified. Although the 45 cold-smoked salmon products shared a core microbiota, a processing plant signature was found. This suggest that the bacterial communities of cold-smoked salmon products are impacted by the processing environment, and this environment could have a negative effect on product quality. The use of a polyphasic approach for seafood products and food processing environments could provide better insights into residential bacteria dynamics and their impact on food safety and quality.

Amplicon sequencing approaches have been widely used in food bacterial ecology. However, choices regarding the methodology can bias results. In this study, bacterial communities associated with cold-smoked salmon products and their processing plant surfaces were monitored via sequencing of the V3-V4 region of the 16S rRNA gene. The impact of DNA extraction protocols, sampling methods (swabbing or sponging) and surface materials on bacterial communities were investigated. alpha and beta diversity analyses revealed that DNA extraction methods mainly influence the observed cold-smoked salmon microbiota composition. Moreover, different DNA extraction methods revealed significant differences in observed community richness and evenness. beta-Proteobacteria: Photobacterium, Serrano and Firmicutes: Brochothrix, Carnobacterium and Staphylococcus were identified as the dominant genera. Surface microbiota richness, diversity and composition were mainly affected by cleaning and disinfection procedures but not by DNA extraction methods. Surface community richness and evenness appeared higher when sampled by sponging compared to swabbing. beta-diversity analyses highlighted that surface topology, cleaning and disinfection and sampling devices seemed to affect the bacterial community composition. The dominant surface bacteria identified were mainly Flayobacteriaceae, beta-Proteobacteria and gamma-Proteobacteria described as fish spoilers such as Acinetobacter, Pseudomonas and Shewanella. DNA extraction and sampling methods can have an impact on sequencing results and the ecological analysis of bacterial community structures. This study confirmed the importance of methodology standardization and the need for analytical validation before 16S rDNA metabarcoding surveys.

Purpose This study aims at designing a lactic starter for caper fermentation isolated from Tunisian fermented vegetables to improve the process and produce consistent and high-quality product. Methods In this study, the lactic starter was isolated by exploring the lactic acid bacteria (LAB) of Tunisian artisanal fermented vegetables. Identification was carried out by partial 16S rRNA gene sequencing. Screening was based on salt tolerance and antagonistic activities against Escherichia coli ATCC 10536 and Enterococcus faecalis ATCC 10541. Caper fermentation was optimized through a full factorial experimental design (2 3 ), by exploring three factors: starter inoculum size, NaCl concentration, and acetate content. Differences in pH values, Total aerobic mesophilic bacteria and LAB counts between the beginning and end of fermentation are selected as responses and corresponding regression coefficients were calculated. Results The lactic microbiota is mainly represented by Lactobacillus plantarum group. Based on salt tolerance and antimicrobial activity, the strain Lactobacillus plantarum F3 was selected as starter for caper fermentation. The effect of NaCl concentration, acetate content, and inoculum size on acidity, total aerobic mesophilic bacteria count, and LAB count after 1 week and 1 month of caper fermentation was studied. Depending on the fermentation time, either 1 week or 1 month, the initial conditions should comprise 0% acetate, 10 8 CFU/mL inoculum, and 5% NaCl for 1 week against 5% acetate, 10 7 CFU/mL inoculum, and 10% NaCl for 1 month lasting caper fermentation. A protocol for caper fermentation was set up ensuring hygienic quality and LAB viability. Conclusion Lb. plantarum F3 was selected as lactic starter for caper fermentation, and initial fermentation conditions were optimized through a full factorial design. This work has shown loss in LAB viability after 1 week of fermentation. Based on results obtained, an optimized fermentation protocol was set up. This protocol ensures LAB survival and high hygienic quality of the product.

Role of agronomic and bread-making practices in sourdough microbial diversity and bread nutritional and organoleptic properties. 7. international symposium on sourdough

Since the Neolithic time, until nowadays, humans have recurrently selected microbial community for making fermented food and beverage. This represents a good opportunity to study the community ecology and evolution of microbial ecosystem during ongoing domestication. Using sourdough bread as a model system and an interdisciplinary approach including bakers, farmers, sociologist, bio-mathematicians and biologists, we analyzed the impact of human on the diversity and evolution of microbial communities in France. Natural sourdough bread is made of wheat flour, water and sourdough. Sourdough is composed of flour, water, bacteria and fungi. Bakers initiate a new sourdough by mixing flour and water, and maintained it by regular feedings with flour and water, a process called back-slopping. Using a social survey of bread-making practices and a microbial ecologist approaches, we showed that bread-making practices impact sourdough microbial species diversity. Farmerbakers maintained different yeast species than bakers. In addition, we revealed convergent phenotypic evolution of sourdough strains of different yeast species for fermentation traits indicating that bakers have independently selected for phenotype of interest regardless of the yeast species. Finally, we realized an experiment of domestication in action by asking four bakers to initiate new sourdoughs with six different flours. The weekly followed up of sourdough species composition revealed that, for each baker, a single yeast and a single bacteria species dominated the community after 3 weeks of back-slopping. Despite the introduction of new bacteria and yeast from the flour at each back-slopping, the dominant species was the one present in the home sourdough indicating that dispersion and selection occurred mostly within the bakery. All together our study highlighted that domestication of microbial community can be a good model to bridge community ecology and evolution, to study the adaptation dynamic and the genetic architecture of fast evolving traits involved in abiotic and biotic interactions.

Using sourdough bread ecosystems as a model and a participatory research approach, we have analysed human impact on the dispersion and selection of lactic acid bacteria and yeasts. In France, microbial diversity associated with bread-making practises has recently been documented. In order to better understand the origin of the sourdough microbial diversity, we analyzed the effect of (i) terroir (ii) wheat varieties, (iii) bakers on sourdough microbial taxonomic and functional diversity. Three populations of old wheat and three varieties of commercial wheat were each grown on three terroirs. For each terroir, grains from the three old populations were mixed and so were grains from the three modern varieties. The flours of the six seeds lots were sent to four different bakers, who initiated and maintained six sourdoughs for three weeks. The sourdoughs were then analyzed by cultural and non-cultural methods. Total yeast counts varied from 5.6 log10 to 8.49 log10 CFU/g while LAB counts varied from 7 log10 to 10.6 log10 CFU/g. By culture-dependent methods, five yeasts species were identified and fifteen acid lactic bacteria species. The composition of the sourdough dominant species varies according to the bakers but does not appear to change according to the origin of the flour. The sourdoughs impact the rising of the dough but the rate of total CO2 release depends mainly on the type of wheat varieties. The nutritional quality of the bread results from the interaction between the sourdough, the type of wheat varieties and the terroir. Overall, house microbiota appears to be the main factor driving sourdough ecosystem microbial diversity but the origin of wheat also impacts bread quality. Our results highlight the role of human and socio-cultural practices in maintaining taxonomic and functional diversity of microbial species.

The growth of food-spoilage and foodborne pathogenic bacteria was inhibited by a nisin Z-producing Lactococcus lactis subsp. lactis KT2W2L as determined by the agar spot test and agar well diffusion assay. The growth of Brochothrix thermosphacta DSMZ 20171(T) and Staphylococcus aureus CIP 76.25 was inhibited when co-cultivated with L lactis subsp. lactis KT2W2L whereas the growth of Escherichia coli CIP 76.24 and Salmonella Enteritidis CIP 813 was not. However, the growth level of E. coli CIP 76.24 and S. Enteritidis CIP 813 co-cultivated with L. lactis subsp. lactis KT2W2L was diminished compared to cultivation without L lactis subsp. lactis KT2W2L. The neutralized cell-free supernatant (NCFS) collected from the culture of L lactis subsp. lactis KT2W2L, cultivated with and without indicator strain, exhibited inhibition zones against the indicator strains as determined by the agar well diffusion assay. The results reported in this study indicate that a nisin Z-producing L lactis subsp. lactis KT2W2L may find application as a bio-preservative for reducing food-spoilage and foodborne pathogens in food products. (C) 2017 Elsevier Ltd. All rights reserved.

Food products can be spoiled by bacteria, as they provide a rich nutrient source with physicochemical parameters, like pH and water activity, compatible with bacterial growth. In addition, the conditions used during food processing and storage, like temperature, addition of ingredients, and the use of modified atmosphere or vacuum packaging, exert a selective pressure that shapes the development of bacterial communities. Consequently, bacterial spoilage depends on the food matrices, on their production processes, and on their storage conditions. The main characteristics of bacterial spoilage of dairy, meat, and seafood products and products of vegetable origin are presented.

An accurate amplified fragment length polymorphism (AFLP) method, including three primer sets for the selective amplification step, was developed to display the phylogenetic position of Photobacterium isolates collected from salmon products. This method was efficient for discriminating the three species Photobacterium phosphoreum, Photobacterium iliopiscarium and Photobacterium kishitanii, until now indistinctly gathered in the P. phosphoreum species group known to be strongly responsible for seafood spoilage. The AFLP fingerprints enabled the isolates to be separated into two main clusters that, according to the type strains, were assigned to the two species P. phosphoreum and P. iliopiscarium. P. kishitanii was not found in the collection. The accuracy of the method was validated by using gyrB-gene sequencing and luxA-gene PCR amplification, which confirmed the species delineation. Most of the isolates of each species were clonally distinct and even those that were isolated from the same source showed some diversity. Moreover, this AFLP method may be an excellent tool for genotyping isolates in bacterial communities and for clarifying our knowledge of the role of the different members of the Photobacterium species group in seafood spoilage.

In order to contribute to the description of sourdough LAB composition, MiSeq sequencing and qPCR methods were performed in association with cultural methods. A panel of 16 French organic bakers and farmer-bakers were selected for this work. The lactic acid bacteria (LAB) diversity of their organic sourdoughs was investigated quantitatively and qualitatively combining (i) Lactobacillus sanfranciscensis-specific qPCR, (ii) global sequencing with MiSeq Illumina technology and (iii) molecular isolates identification. In addition, LAB and yeast enumeration, pH, Total Titratable Acidity, organic acids and bread specific volume were analyzed. Microbial and physico-chemical data were statistically treated by Principal Component Analysis (PCA) and Hierarchical Ascendant Classification (HAC). Total yeast counts were 6 log10 to 7.6 log10 CFU/g while LAB counts varied from 7.2 log10 to 9.6 log10 CFU/g. Values obtained by L. sanfranciscensis-specific qPCR were estimated between 7.2 and 10.3 log10 CFU/g, except for one sample at 4.4 log10 CFU/g. HAC and PCA clustered the sixteen sourdoughs into three classes described by their variables but without links to bakers' practices. L. sanfranciscensis was the dominant species in 13 of the 16 sourdoughs analyzed by Next Generation Sequencing (NGS), by the culture dependent method this species was dominant only in only 10 samples. Based on isolates identification, LAB diversity was higher for 7 sourdoughs with the recovery of L. curvatus, L. brevis, L. heilongjiangensis, L. xiangfangensis, L. koreensis, L. pontis, Weissella sp. and Pediococcus pentosaceus, as the most representative species. L. koreensis, L. heilongjiangensis and L. xiangfangensis were identified in traditional Asian food and here for the first time as dominant in organic sourdough. This study highlighted that L. sanfranciscensis was not the major species in 6/16 sourdough samples and that a relatively high LAB diversity can be observed in French organic sourdough.

Doklu is a maize-based spontaneously fermented dough produced and consumed in parts of West Africa, particularly in Cote d'Ivoire. The characterization of the microbial ecosystem of doklu was carried out using a polyphasic approach. First, culture-dependent methods were used for bacterial enumeration and the phenotypic and molecular identification of 250 lactic acid bacteria (LAB) isolates. Then, culture-independent methods, including PCR-TTGE (V3 region of the 16S rRNA gene), provided a fingerprinting of bacterial DNA directly extracted from doklu. Bio preservative abilities were also tested and strains producing antimicrobial compounds were genotyped using PFGE. During maize dough fermentation, LAB became dominant and their load increased from 4.2 +/- 0.2 log CFU/g to 9.0 +/- 0.7 log CFU/g only after 48 h. Culture-dependent methods highlighted the presence of five LAB groups with the species Lactobacillus plantarum (28%), Lactobacillus fermentum (41.6%), Pediococcus acidilactici (6.8%), Pediococcus pentosaceus (18%) et Weissella cibaria (5.6%), succeeding during the fermentation. Lb. fermentum being practically the only species present at the end of fermentation, is with Lb. plantarum, the predominant species of fermenting dough. Culture-independent analysis underlined the undoubted role of Lb. fermentum, actively involved in the dough fermentation. These Lb. fermentum species, with a diversity of strains also showed important antimicrobial activity, due to production of bacteriocins. Being able to produce antimicrobial compounds, Lb. fermentum species may act as both bio protective culture as well as fermenting agent in cereal products and could be exploited to create functional starter cultures. (C) 2015 Elsevier Ltd. All rights reserved.

Campylobacteriosis is the most frequently reported zoonotic disease in humans in the EU since 2005. As chicken meat is the main source of contamination, reducing the level of Campylobacter in broiler chicken will lower the risk to consumers. The aim of this project was to evaluate the ability of Lactobacillus salivarius SMXD51 to control Campylobacter jejuni in broilers and to investigate the mechanisms that could be involved. Thirty broilers artificially contaminated with C. jejuni were treated by oral gavage with MRS broth or a bacterial suspension (107CFU) of Lb. salivarius SMXD51 (SMXD51) in MRS broth. At 14 and 35days of age, Campylobacter and Lb. salivarius loads were assessed in cecal contents. The impact of the treatment on the avian gut microbiota at day 35 was also evaluated. At day 14, the comparison between the control and treated groups showed a significant reduction (P<0.05) of 0.82 log. After 35days, a significant reduction (P<0.001) of 2.81 log in Campylobacter loads was observed and 73% of chickens treated with the culture exhibited Campylobacter loads below 7log10CFU/g. Taxonomic analysis revealed that SMXD51 treatment induced significant changes (P<0.05) in a limited number of bacterial genera of the avian gut microbiota and partially limited the impact of Campylobacter on Anaerotruncus sp. decrease and Subdoligranulum sp. increase. Thus, SMXD51 exhibits an anti-Campylobacter activity in vivo and can partially prevent the impact of Campylobacter on the avian gut microbiota.

Campylobacteriosis is the most common cause of bacterial gastroenteritis worldwide. Campylobacter species involved in this infection usually include the thermotolerant species Campylobacter jejuni. The major reservoir for C. jejuni leading to human infections is commercial broiler chickens. Poultry flocks are frequently colonized by C. jejuni without any apparent symptoms. Risk assessment analyses have identified the handling and consumption of poultry meat as one of the most important sources of human campylobacteriosis, so elimination of Campylobacter in the poultry reservoir is a crucial step in the control of this foodborne infection. To date, the use of probiotics has demonstrated promising results to reduce Campylobacter colonization. This review provides recent insights into methods used for probiotic screening to reduce the prevalence and colonization of Campylobacter at the farm level. Different eukaryotic epithelial cell lines are employed to screen probiotics with an anti-Campylobacter activity and yield useful information about the inhibition mechanism involved. These in vitro virulence models involve only human intestinal or cervical cell lines whereas the use of avian cell lines could be a preliminary step to investigate mechanisms of C. jejuni colonization in poultry in the presence of probiotics. In addition, in vivo trials to evaluate the effect of probiotics on Campylobacter colonization are conducted, taking into account the complexity introduced by the host, the feed, and the microbiota. However, the heterogeneity of the protocols used and the short time duration of the experiments lead to results that are difficult to compare and draw conclusions at the slaughter-age of broilers. Nevertheless, the combined approach using complementary in vitro and in vivo tools (cell cultures and animal experiments) leads to a better characterization of probiotic strains and could be employed to assess reduced Campylobacter spp. colonization in chickens if some parameters are optimized.

Lactobacillus sanfranciscensis is the predominant key lactic acid bacterium in traditionally fermented sourdoughs. Despite its prevalence, sourdough and their related breads could be different regarding their physicochemical and sensorial characteristics. The intraspecific diversity of L. sanfranciscensis might explain these observations. Fifty-nine strains isolated from French sourdoughs were typed by a polyphasic approach including Multilocus Sequence Typing (MLST) and Pulsed-field Gel Electrophoresis (PFGE), in order to study their genotypic diversity. MLST scheme can be reduced from six to four gene fragments (gdh, gyrA, nox and pta) without a major loss of discrimination between strains. The genes mapA and pgmA are not good candidates for inclusion in an MLST scheme to type L. sanfranciscensis strains, as they could not be amplified for a set of 18 strains among the 59 studied. This method revealed 20 sequence types (STs). Of these, 19 STs were grouped in one clonal complex, showing a strong relatedness between these strains. PFGE using SmaI discriminated 41 pulsotypes and so distinguished isolates better than the MLST scheme. Both genotypic methods indicate a low diversity between strains isolated from the same sourdough and a higher diversity between strains isolated from different sourdoughs, suggesting an influence of baker practices and/or environmental conditions on the selection of strains. The use of these two methods targeting genetic variations gives an optimal genotypic characterization of L.sanfranciscensis strains.