Inducible gene expression in Lactobacillus reuteri LTH5531 during type II sourdough fermentation

Biodiversity and Safety Assessment of Half-Century Preserved Natural Starter Cultures for Pecorino Romano PDO Cheese

The use of biodiverse autochthonous natural starter cultures to produce typical and PDO cheeses contributes to establishing a link between products and territory of production, which commercial starters, constituted by few species and strains, are not able to. The purpose of this work was the assessment of biodiversity, at strain level, and safety of natural scotta-innesto cultures whose use is mandatory for the Pecorino Romano PDO cheese manufacturing, according to its product specification. The biodiversity of three scotta-innesto, collected in the 1960s and preserved in lyophilised form, was assessed by molecular biotyping using both PFGE and (GTG)₅ rep-PCR profiling on 209 isolates belonging to Streptococcus thermophilus (30), Lactobacillus delbrueckii subsp. lactis (72), Enterococcus faecium (87), and Limosilactobacillus reuteri (20), revealing high biodiversity, at the strain level, in the cultures. The cultures’ safety was proved through a new approach assessing phenotypic and molecular antibiotic resistance of the cultures in toto, instead of single strains, while the safety of Enterococcus faecium isolates was investigated according to EFSA guidelines. The use of natural biodiverse cultures for the production of microbial starters for typical and PDO cheeses, such as Pecorino Romano, could be an opportunity for recovering the cheese microbiota biodiversity lost during years of commercial starters use.

Reprogramming Probiotic Lactobacillus reuteri as a Biosensor for Staphylococcus aureus Derived AIP-I Detection

Gram-positive Staphylococcus aureus infection that results in pneumonia, urinary tract infection, and in severe cases, sepsis, has recently been classified as a serious threat to public health. Rapid and cost-effective detection of these infections are costly and time-consuming. Here, we present probiotic lactic acid bacteria engineered to detect autoinducer peptide-I (AIP-I), a quorum sensing molecule produced by Staphylococcus sp. during pathogenesis. We achieved this by adapting the well-characterized agr quorum sensing ( agrQS) from Staphylococcus aureus into Lactobacillus reuteri. The engineered biosensor is able to detect AIP-I levels in the nanomolar to micromolar range. We further investigated the function of the biosensor to detect real-time changes in AIP-I levels to understand the dynamics of Staphylococcus aureus under various strenuous conditions. The developed sensors would be useful for detection of Staphylococcus contamination in hospital settings and for high-throughput drug screening.

Evaluation of growth, metabolism and production of potentially bioactive components during fermentation of barley with Lactobacillus reuteri

Eighteen bacterial isolates from millet, buckwheat and rye flour were identified as Lactobacillus reuteri. Genomic fingerprinting (rep-PCR) revealed that they represented five strains and phylogenetic analyses using multi locus sequence analysis (MLSA) showed that all clustered with strains of rodent origin. Two strains (SU12-3 and SU18-3) from different phylogenetic clades were used in fermentations of six varieties of barley, both untreated and heat-treated (with inactivated indigenous enzymes) flour. They were compared with two probiotic strains of human origin (DSM 17938 and ATCC PTA 6475), one previously isolated sourdough strain (LTH 5531) and one strain of Lactobacillus plantarum (36E). Analyses of growth (CFU) and metabolism (1H-NMR) revealed differences at species level, with L. plantarum showing a higher capacity to assimilate nutrients without help of the cereal enzymes. Similarities were observed between L. reuteri strains isolated from sourdough, while the greatest differences between L. reuteri strains were observed between strains 6475 and 17938. Multivariate analysis of the metabolic profiles revealed clear clustering according to flour treatment, species of bacteria and barley variety and to some extent also bacterial strain. Possible bioactive compounds such as γ-aminobutyric acid (GABA), 1,3- propanediol (sign of reuterin production) and histamine were identified and quantified.

The transcriptional response of Lactobacillus sanfranciscensis DSM 20451T and its tcyB mutant lacking a functional cystine transporter to diamide stress

As a result of its strong adaptation to wheat and rye sourdoughs, Lactobacillus sanfranciscensis has the smallest genome within the genus Lactobacillus. The concomitant absence of some important antioxidative enzymes and the inability to synthesize glutathione suggest a role of cystine transport in maintenance of an intracellular thiol balance. Diamide [synonym 1,1'-azobis(N,N-dimethylformamide)] disturbs intracellular and membrane thiol levels in oxidizing protein thiols depending on its initial concentration. In this study, RNA sequencing was used to reveal the transcriptional response of L. sanfranciscensis DSM 20451(T) (wild type [WT]) and its ΔtcyB mutant with a nonfunctional cystine transporter after thiol stress caused by diamide. Along with the different expression of genes involved in amino acid starvation, pyrimidine synthesis, and energy production, our results show that thiol stress in the wild type can be compensated through activation of diverse chaperones and proteases whereas the ΔtcyB mutant shifts its metabolism in the direction of survival. Only a small set of genes are significantly differentially expressed between the wild type and the mutant. In the WT, mainly genes which are associated with a heat shock response are upregulated whereas glutamine import and synthesis genes are downregulated. In the ΔtcyB mutant, the whole opp operon was more highly expressed, as well as a protein which probably includes enzymes for methionine transport. The two proteins encoded by spxA and nrdH, which are involved in direct or indirect oxidative stress responses, are also upregulated in the mutant. This work emphasizes that even in the absence of definitive antioxidative enzymes, bacteria with a small genome and a high frequency of gene inactivation and elimination use small molecules such as the cysteine/cystine couple to overcome potential cell damage resulting from oxidative stress.

Selection of in vivo expressed genes of Escherichia coli O157:H7 strain EDL933 in ground meat under elevated temperature conditions

Enterohemorrhagic Escherichia coli O157:H7 strains are important foodborne pathogens that are often transmitted to humans by the ingestion of raw or undercooked meat of bovine origin. To investigate adaptation of this pathogen during persistence and growth in ground meat, we established an in vivo expression technology model to identify genes that are expressed during growth in this food matrix under elevated temperatures (42°C). To improve on the antibiotic-based selection method, we constructed the promoter trap vector pAK-1, containing a promoterless kanamycin resistance gene. A genomic library of E. coli O157:H7 strain EDL933 was constructed in pAK-1 and used for promoter selection in ground meat. The 20 in vivo expressed genes identified were associated with transport processes, metabolism, macromolecule synthesis, and stress response. For most of the identified genes, only hypothetical functions could be assigned. The results of our study provide the first insights into the complex response of E. coli O157:H7 to a ground meat environment under elevated temperatures and establish a suitable vector for promoter studies or selection of in vivo induced promoters in foods such as ground meat.

Impact of ecological factors on the stability of microbial associations in sourdough fermentation

The limits for the stability of the microbial association 1 (Lactobacillus sanfranciscensis and Candida humilis) and association 2 (Lactobacillus reuteri, Lactobacillus johnsonii and Issatchenkia orientalis) during sourdough fermentation were evaluated by investigating the effects of the ecological factors substrate, refreshment time, temperature, amount of backslopping and competing species in different combinations on their growth. Sourdoughs were fermented in 28 batches under different conditions using the associations and possible competing strains as starters. The dominating microbiota was characterized by bacteriological culture, rRNA gene sequence analysis and RAPD-PCR. Association 1 was found to be competitive in doughs with rye and wheat flour at temperatures between 20 and 30 °C, refreshment times of 12 and 24 h, amounts of backslopping dough from 5 to 20% and against all competing lactic acid bacteria and yeasts. The processing parameters for the competitiveness of the association 2 were temperatures of 35-40 °C, refreshment times of 12-24 h and the substrates rye bran, wheat and rye flour, but not in every case. Issatchenkia orientalis could only grow when enough oxygen was available. Its cell counts fell rapidly under the limit of detection when using high amounts of doughs (small ratio of surface to volume) and refreshment times of 12 h. In conclusion, the results demonstrated that the two associations were remarkably stable under most of the investigated process conditions.

Metabolic impact and potential exploitation of the stress reactions in lactobacilli

Lactic acid bacteria (LAB) are a functionally related group of organisms known primarily for their bioprocessing roles in food and beverages. The largest variety of metabolic properties is found in the group of lactobacilli the vast majority of which has been isolated in cereal environments, namely sourdoughs, in which their role ranges from sporadic contaminants to major fermentative flora. Growth or survival in each of these environmental niches depends on the ability of the organism to sense and respond to varying conditions such as temperature, pH, nutrients availability and cell population density. Fermentation process conditions, including temperature range, dough yield, oxygen, pH as well as the amount and composition of starter cultures, determine the cells' metabolic response. In fact, the exposure of microbial cells to stressful conditions during fermentation involves a broad transcriptional response with many induced or repressed genes. The complex network of such responses, involving several metabolic activities will reflect upon the metabolome of the fermentative flora, and thus on the composition and organoleptic properties of the final products. This review shall provide insight into stress response mechanisms and delineate the vast potential residing in the exploitation of the stress dependent metabolome of LAB focusing on bacteria of the sourdough environment as one of the richest sources of lactobacilli.

The early response to acid shock in Lactobacillus reuteri involves the ClpL chaperone and a putative cell wall-altering esterase

To be able to function as a probiotic, bacteria have to survive the passage through the gastrointestinal tract. We have examined survival and gene expression of Lactobacillus reuteri ATCC 55730 after a sudden shift in environmental acidity to a pH close to the conditions in the human stomach. More than 80% of the L. reuteri cells survived at pH 2.7 for 1 h. A genomewide expression analysis experiment using microarrays displayed 72 differentially expressed genes at this pH. The early response to severe acid shock in L. reuteri differed from long-term acid adaptation to milder acid stress studied in other lactic acid bacteria. The genes induced included the following: clpL, genes putatively involved in alterations of the cell membrane and the cell wall; genes encoding transcriptional regulators; phage genes; and genes of unknown function. Two genes, clpL, encoding an ATPase with chaperone activity, and lr1516, encoding a putative esterase, were selected for mutation analyses. The mutants were significantly more sensitive to acid than the wild type was. Thus, these genes could contribute to the survival of L. reuteri in the gastrointestinal tract.

Identification of Lactobacillus sakei genes induced during meat fermentation and their role in survival and growth

Lactobacillus sakei is a lactic acid bacterium that is ubiquitous in the food environment and is one of the most important constituents of commercial meat starter cultures. In this study, in vivo expression technology (IVET) was applied to investigate gene expression of L. sakei 23K during meat fermentation. The IVET vector used (pEH100) contained promoterless and transcriptionally fused reporter genes mediating beta-glucuronidase activity and erythromycin resistance. A genomic library of L. sakei 23K was established, and the clones were subjected to fermentation in a raw-sausage model. Fifteen in carne-induced fusions were identified. Several genes encoded proteins which are likely to contribute to stress-related functions. One of these genes was involved in acquisition of ammonia from amino acids, and the remaining either were part of functionally unrelated pathways or encoded hypothetical proteins. The construction and use of isogenic mutants in the sausage model suggested that four genes have an impact on the performance of L. sakei during raw-sausage fermentation. Inactivation of the heat shock regulator gene ctsR resulted in increased growth, whereas knockout of the genes asnA2, LSA1065, and LSA1194 resulted in attenuated performance compared to the wild-type strain. The results of our study are the first to provide an insight into the transcriptional response of L. sakei when growing in the meat environment. In addition, this study establishes a molecular basis which allows investigation of bacterial properties that are likely to contribute to the ecological performance of the organism and to influence the final outcome of sausage fermentation.

Biodiversity and identification of sourdough lactic acid bacteria

This review deals with recent developments on the biodiversity of sourdough lactic acid bacteria (LAB) and the recent description of new sourdough LAB species. One of the outcomes of biodiversity studies of particular sourdough ecosystems throughout Europe is the description of new taxa of LAB. During the last 3 years, several new LAB species have been isolated from traditional sourdoughs: Lactobacillus mindensis, Lactobacillus spicheri, Lactobacillus rossiae, Lactobacillus zymae, Lactobacillus acidifarinae, Lactobacillus hammesii, and Lactobacillus nantensis. Some of these species have been described on one single isolate only. Isolation of novel taxa mainly depends on the cultivation approach used, i.e. (selective) incubation media and conditions. The distribution of the taxa of LAB is highly variable from one sourdough ecosystem to another. Therefore, it is difficult to define correlations between population composition and both the type of sourdough or the geographic location. Identification of isolated strains needs a polyphasic approach, including a combination of phenotypic and genotypic methods, the latter often based on the polymerase chain reaction (PCR) and encompassing 16S rRNA sequencing and DNA-DNA hybridizations. A main obstacle in current identification approaches of LAB strains is the lack of a robust and exchangeable identification system for all LAB species. Recent studies based on complete genomes have provided the basis for establishing sets of genes useful for multi-locus sequence analysis (MLSA). Monitoring the population dynamics of sourdough ecosystems can be performed by both culture-dependent (plating and incubation) and culture-independent (e.g. PCR-Denaturing Gradient Gel Electrophoresis) methods. Although highly valuable for community fingerprinting, culture-independent methods do not always yield precise quantitative information.