Carrot (Daucus carota L.) production is challenged by various phytopathogens, including Berkeleyomyces basicola, responsible for black root rot. Current control measures are limited, prompting interest in sustainable biopreservation approaches leveraging beneficial microorganisms. This study evaluated the biopreservation potential of several lactic acid bacteria (LAB) strains from the Agroscope Culture Collection and bacteria newly isolated from carrots against B. basicola and other carrot phytopathogens, namely Alternaria radicina, Rhizoctonia solani and Sclerotinia sclerotiorum. Results highlighted the superior performance of strains isolated from carrots, including Leuconostoc mesenteroides, Serratia plymuthica and Raoultella terrigena in inhibiting B. basicola mycelial growth and spore germination compared to the previously isolated LAB strains from the Agroscope Culture Collection. Interestingly, non-LAB strains, particularly Serratia plymuthica Sp1, exhibited broad-spectrum antifungal activity and sustained protection of carrots while used as postharvest treatment. These findings emphasize the value of exploring the microbiota of the host plant to be protected to find new agents suitable for biocontrol solutions. While LAB strains showed promising results in in vitro assays, S. plymuthica Sp1 emerged as a highly effective candidate for postharvest disease management. Future research should focus on optimizing the application and formulation of S. plymuthica for large-scale use, ensuring its compatibility with diverse carrot varieties and storage environments. This work contributes to the development of environmentally friendly strategies to reduce postharvest losses and enhance sustainability in food production.

The function of the aminotransferase Aat (GenBank Protein WP_159211138) from Pediococcus acidilactici FAM 18098 was studied in vivo. For this purpose, the gene was replaced with an erythromycin resistance gene using the temperature-sensitive Escherichia coli-Pediococcus shuttle plasmid pSET4T_Δaat. The knockout was verified by PCR and genome sequencing. Subsequently, the differences between the metabolism of the knockout and of the wild-type strain were investigated by determining the free amino acids and organic acids in culture supernatants. It was found that the knockout mutant no longer synthesized 3-phenyllactic acid (PLA) and 4-hydroxyphenyllactic acid (HPLA). Additionally, the mutant strain no longer catabolized phenylalanine. Metabolic pathway analysis using the KEGG database indicate that P. acidilactici cannot synthesize α-ketoglutarate that is a predominant amino-group acceptor in many transamination reactions. To study the transfer of the amino group of phenylalanine, the wild-type strain was incubated with [15N] phenylalanine. Mass spectrometry showed that during fermentation, [15N] alanine was formed, indicating that pyruvic acid is an amino group acceptor in P. acidilactici. The present study shows that Aat plays a crucial role in PLA/HPLA biosynthesis and pyruvic acid is an amino acceptor in transamination reactions in P. acidilactici.

Additional file 2: Table S1. Concentrations of the free amino acids (mmol/L) in broth fermented with different pediococcal strains. The values of two independently performed experiments are shown. Basal broth stands for the non-inoculated medium. (AABA: α-aminobutyrate, GABA: γ-aminobutyrate, FAA: free amino acids).

During cheese ripening, the bacterial strain Pediococcus acidilactici FAM18098 produces the non-proteinogenic amino acid, α-aminobutyrate (AABA). The metabolic processes that lead to the biosynthesis of this compound are unknown. In this study, 10 P. acidilactici, including FAM18098 and nine Pediococcus pentosaceus strains, were screened for their ability to produce AABA. All P. acidilactici strains produced AABA, whereas the P. pentosaceus strains did not. The genomes of the pediococcal strains were sequenced and searched for genes encoding aminotransferases to test the hypothesis that AABA could result from the transamination of α-ketobutyrate. A GenBank and KEGG database search revealed the presence of a species-specific aminotransferase in P. acidilactici. The gene was cloned and its gene product was produced as a His-tagged fusion protein in Escherichia coli to determine the substrate specificity of this enzyme. The purified recombinant protein showed aminotransferase activity at pH 5.5. It catalyzed the transfer of the amino group from leucine, methionine, AABA, alanine, cysteine, and phenylalanine to the amino group acceptor α-ketoglutarate. Αlpha-ketobutyrate could replace α-ketoglutarate as an amino group acceptor. In this case, AABA was produced at significantly higher levels than glutamate. The results of this study show that P. acidilactici possesses a novel aminotransferase that might play a role in cheese biochemistry and has the potential to be used in biotechnological processes for the production of AABA.

There is limited information about the contribution of Pediococcus acidilactici, a nonstarter lactic acid bacteria, to cheese ripening and flavour development. Model Tilsit-type and Gruyere-type cheeses were produced using P. acidilactici FAM18098 as an adjunct. The adjunct did not influence the cheese manufacturing processes. The pediococcal log counts ranged from 7.0 to 8.0 cfu g(-1) after 90 and 120 days of ripening. P. acidilactici produced ornithine, a result of arginine metabolism by the arginine deiminase pathway, and alpha-aminobutyrate and alanine while simultaneously metabolising serine and threonine. The analysis of the volatile compounds in the cheeses showed that higher acetate, 2-butanone, and 2-butanol levels and lower diacetyl levels were present in the cheeses produced with P. acidilactici than in the control cheeses. The study illustrates that P. acidilactici can influence amino acid metabolism in cheese; further, ornithine, alpha-aminobutyrate, and acetate can serve as indicators for the presence of this species. (C) 2019 The Author(s). Published by Elsevier Ltd.

In the manufacture of traditional cheese varieties, processing fresh milk that has been treated as little as possible is crucial. Preserving the microbiome and the activity of the original enzymes in the raw milk to the greatest extent possible allows these cheeses to retain their original character. This objective conflicts with the growing demands placed on products in terms of food safety. The present literature search addresses the influence of the pre-treatment of cheesemaking milk on the food safety and quality of ripened cheeses, with particular focus on heat treatment, bactofugation, and microfiltration.

If self-sufficiency in vegetable protein for the human diet is to be increased, the issue should be considered as comprehensively as possible. This study presents a systemic analysis of the situation in Switzerland, showing which protein-rich crops are most suited to sustainable and organic farming, highlighting their nutritional potential, and indicating the necessary steps for processing them into protein concentrates and isolates suitable for the production of meat alternatives.

Milk and dairy products are rich in nutrients and are therefore habitats for various microbiomes. However, the composition of nutrients can be quite diverse, in particular among the sulfur containing amino acids. In milk, methionine is present in a 25-fold higher abundance than cysteine. Interestingly, a fraction of strains of the species L. paracasei - a flavor-enhancing adjunct culture species - can grow in medium with methionine as the sole sulfur source. In this study, we focus on genomic and evolutionary aspects of sulfur dependence in L. paracasei strains. From 24 selected L. paracasei strains, 16 strains can grow in medium with methionine as sole sulfur source. We sequenced these strains to perform gene-trait matching. We found that one gene cluster - consisting of a cysteine synthase, a cystathionine lyase, and a serine acetyltransferase - is present in all strains that grow in medium with methionine as sole sulfur source. In contrast, strains that depend on other sulfur sources do not have this gene cluster. We expanded the study and searched for this gene cluster in other species and detected it in the genomes of many bacteria species used in the food production. The comparison to these species showed that two different versions of the gene cluster exist in L. paracasei which were likely gained in two distinct events of horizontal gene transfer. Additionally, the comparison of 62 L. paracasei genomes and the two versions of the gene cluster revealed that this gene cluster is mobile within the species.

MultipleSi l’on veut accroitre l’autosuffisance en proteines vegetales destinees a l’alimentation humaine, il importe d’aborder la question avec une vision aussi globale que possible. Cette etude propose une analyse systemique de la situation en Suisse. Elle montre quelles plantes riches en proteines se pretent le mieux a une culture a la fois durable et ecologique, puis discute leur potentiel nutritionnel ainsi que les procedes permettant de les transformer en concentrats et isolats proteiques, qui sont a leur tour adaptes a la production de substituts de viande. francaisIf self-sufficiency in vegetable protein for the human diet is to be increased, the issue should be considered as comprehensively as possible. This study presents a systemic analysis of the situation in Switzerland, showing which protein-rich crops are most suited to sustainable and organic farming, highlighting their nutritional potential, and indicating the necessary steps for processing them into protein concentrates and isolates suitable for the production of meat alternatives. italianoSe si vuole aumentare l’autonomia d’approvvigionamento di proteine vegetali per l’alimentazione umana, occorre adottare un approccio globale. Il presente studio analizza la situazione in Svizzera in modo sistemico, illustrando quali piante ricche in proteine sono particolarmente indicate per la coltura sostenibile ed ecologica. Descrive quindi quale sia il loro potere nutrizionale e quali processi siano necessari per trasformarle in concentrati e isolati proteici che si prestano alla fabbricazione di sostituti della carne.

Lactobacillus helveticus, a lactic acid bacterium, is an important species in food fermentation, e.g., cheesemaking, and is considered beneficial to human health. We developed a quantitative real-time polymerase chain reaction (qPCR) method for the detection and quantification of L helveticus in dairy products. The method uses a set of target-specific PCR primers and a fluorogenic probe and amplifies a part of the pheS gene that encodes the alpha subunit of the phenyalanine-tRNA synthetase. All 24 L helvetiCus strains tested were qPCR positive; no signal was observed for 23 strains belonging to closely related species. The limit of detection was ten copies per reaction and the assay covered a linear dynamic range of eight logs. The method was used to detect and enumerate L. helveticus in milk and cheese during ripening; therefore it can be used to study the temporal and spatial distribution of L. helveticus during cheese manufacturing and ripening. (C) 2016 The Author(s). Published by Elsevier Ltd.

Histamine in food can cause intolerance reactions in consumers. Lactobacillus parabuchneri (L. parabuchneri) is one of the major causes of elevated histamine levels in cheese. Despite its significant economic impact and negative influence on human health, no genomic study has been published so far. We sequenced and analyzed 18 L. parabuchneri strains of which 12 were histamine positive and 6 were histamine negative. We determined the complete genome of the histamine positive strain FAM21731 with PacBio as well as Illumina and the genomes of the remaining 17 strains using the Illumina technology. We developed the synteny aware ortholog finding algorithm SynOrf to compare the genomes and we show that the histidine decarboxylase (HDC) gene cluster is located in a genomic island. It is very likely that the HDC gene cluster was transferred from other lactobacilli, as it is highly conserved within several lactobacilli species. Furthermore, we have evidence that the HDC gene cluster was transferred within the L. parabuchneri species.

The manufacture of traditional Swiss-type cheeses adheres to strict rules, so as to guarantee quality and purity of the end product. This raises production costs and means consumers pay more. It also opens the door to cut-rate forgeries claiming to be made to the stringent standards and causing considerable economic losses to the entire dairy sector. In order to combat product counterfeiting, Agroscope has developed proof-of-origin cultures that allow the identification of copycats. Carefully selected lactic acid bacteria, having uniquely located insertion sequence elements, are proliferated by fermentation and subsequently dried by lyophilization. The proof-of-origin culture is added during the cheese production process and sustains maturation. These so-called 'biological markers' can be traced using polymerase chain reaction (PCR) methods, which allow authentication even if the cheese is cut into pieces or grated. They do not lead to any alteration of the cheese's taste or texture, and are compatible with the strict 'protected designation of origin' (PDO) specifications. The proof-of-origin cultures are used for the protection of several traditional Swiss-cheese varieties, such as Emmental PDO, Tête de Moine PDO, and Appenzeller(®). A market survey of Emmental PDO showed that the system is effective in revealing fraud and has the power to enforce corrective measures.

Dans la fabrication des fromages traditionnels suisses, la transformation du lait frais, traite avec le plus de menagement possible, est importante. Grâce a la preservation aussi complete que possible du microbiome et de l’activite enzymatique du lait cru, ces fromages conservent leurs caracteristiques d’origine. Toutefois, cet objectif entre en conflit avec les exigences croissantes de securite alimentaire. Cette revue de litterature porte sur l’influence du pretraitement du lait de fromagerie, en particulier du traitement thermique, de la bactofugation et de la microfiltration, en vue de garantir la securite et la qualite des fromages.