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Wuthrich D.,Swiss Institute of Bioinformatics | Berthoud H.,Institute for Food science | Wechsler D.,Institute for Food science | Eugster E.,Institute for Food science | And 2 more authors.
Frontiers in Microbiology | Year: 2017

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. © 2017 Wüthrich, Berthoud, Wechsler, Eugster, Irmler and Bruggmann.


Shani Levi C.,Technion - Israel Institute of Technology | Goldstein N.,Technion - Israel Institute of Technology | Portmann R.,Institute for Food science | Lesmes U.,Technion - Israel Institute of Technology
Food Hydrocolloids | Year: 2017

World ageing is a growing world concern to which dietary solutions may offer effective measures to tackle malnutrition and support a high quality of life. This study applied a dynamic in vitro model mimicking adult or elderly gastro-duodenal digestion, coupled with proteomic analyses to interrogate the differences in the breakdown of an enteral nutrition formula as well as purified α-lactalbumin (α-lac), β-lactoglobulin (β-lg) and lactoferrin (LF). First, the importance of gastric lipase and various age-related differences in gastro-intestinal conditions (e.g. gastric pH profiles) is shown. Droplet sizing and fluorescent microscopy substantiate emulsion coalescence is favored under adult conditions while flocculation is dominant under elderly conditions. SDS-PAGE analyses of digesta also substantiate differences between adults and seniors in terms of protein breakdown. LC-MS proteomic analyses reveal that digesta samples differ in the incidence of amino acids therein. Comparing proteomic data to databases of known bioactive peptides reveals that β-lg and α-lac may generate more bioactive peptides under adult conditions contrary to LF, which was found to be a better source for bioactive peptides under elderly gut conditions. In addition, proteomic data was mined using PeptideRanker, a bioinformatic tool, in an attempt to identify novel peptide candidates. These efforts generated lists of potentially novel bioactive peptides with a bioactivity probability exceeding 0.6 and in some cases even having a bioactivity probability exceeding 0.9. This study brings forward new information regarding lipids and proteins digestive fate of enteral formula and whey proteins in the elderly gut that stimulate the need for further investigations. © 2017 Elsevier Ltd


Gabioud Rebeaud S.,Institute for Food science | Gasser Agroscope F.,Institute For Lebensmittelwissenschaften Ilm
European Journal of Horticultural Science | Year: 2015

Two new tools for better preservation of fruit quality have been developed in recent years, the treatment of apples with 1-MCP and dynamic controlled atmosphere storage (DCA). The effect of 1-MCP treatment and DCA on ethylene production and quality of ‘Golden Delicious’ apples harvested at two different ripening stages was evaluated in our study over two consecutive years. 1-MCP treatment delayed the climacteric increase of ethylene production and led to better retention of quality during RA- and ULO-storage and subsequent shelf life compared to non-treated apples. In order to achieve the optimum effect of 1-MCP, the treatment must be carried out within 7 days after harvest, as recommended by the supplier of 1-MCP. In most cases, DCA improved quality retention during storage in terms of fruit firmness and acidity compared to ULO-storage. The use of the two methods depends on the cul-tivars stored and conditions such as the infrastructure of the storage facility and type of handling and marketing of the apples. © ISHS 2015.


Weissbrodt D.G.,Ecole Polytechnique Federale de Lausanne | Weissbrodt D.G.,Urban Water Engineering | Weissbrodt D.G.,Eawag - Swiss Federal Institute of Aquatic Science and Technology | Shani N.,Ecole Polytechnique Federale de Lausanne | And 2 more authors.
FEMS Microbiology Ecology | Year: 2014

Intensive nutrient removal from wastewater in anaerobic-aerobic systems using granular sludge should rely on optimal balances at biofilm and microbial ecology levels. This study targets the impacts of reactor characteristics and fluctuations in operation conditions on nutrient removal and bacterial community structures by means of microbial and numerical ecology methods. The dynamics of both predominant and accompanying populations were investigated with high resolution on temporal and phylogenetic scales in two reactors operated during 5 months with synthetic wastewater. Multivariate analyses highlighted significant correlations from process to microbial scales in the first reactor, whereas nitrification and phosphorus removal might have been affected by oxygen mass transfer limitations with no impact at population level in the second system. The bacterial community continuum of the first reactor was composed of two major antagonistic Accumulibacter-Nitrosomonas-Nitrospira and Competibacter-Cytophaga-Intrasporangiaceae clusters that prevailed under conditions leading to efficient P- (> 95%) and N-removal (> 65%) and altered P- (< 90%) and N-removal (< 60%), respectively. A third cluster independent of performances was dominated by Xanthomonadaceae affiliates that were on average more abundant at 25 °C (31 ± 5%) than at 20 °C (22 ± 4%). Starting from the physiological traits of the numerous phylotypes identified, a conceptual model is proposed as a base for functional analysis in the granular sludge microbiome and for future investigations with complex real wastewater. © 2014 Federation of European Microbiological Societies.


Johler S.,Institute for Food Safety and Hygiene | Giannini P.,Cantonal Laboratory | Jermini M.,Cantonal Laboratory | Hummerjohann J.,Institute for Food science | And 2 more authors.
Toxins | Year: 2015

Staphylococcal food poisoning represents the most prevalent foodborne intoxication worldwide. It is caused by oral intake of enterotoxins preformed by Staphylococcus aureus in food. The relevance of newly described enterotoxins in outbreaks of staphylococcal food poisoning is controversially discussed. Although the staphylococcal enterotoxins SEG, SEI, SEM, SEN, and SEO elicit emesis in a monkey feeding assay, there has been no conclusive proof of their emetic activity in humans. In this study, we provide further evidence suggesting that one of these enterotoxins or a combination of SEG, SEI, SEM, SEN, and SEO cause staphylococcal food poisoning. We investigated two outbreaks registered with the Swiss Federal Office of Public Health, in which only Staphylococcus aureus strains harboring the egc cluster, including seg, sei, sem, sen, and seo linked to typical signs of staphylococcal food poisoning were isolated. The outbreaks were caused by consumption of raw goat cheese and semi-hard goat cheese, and were linked to strains assigned to CC45 (agr type I) and CC9 (agr type II), respectively. These outbreaks provide further evidence that newly-described staphylococcal enterotoxins are likely to cause staphylococcal food poisoning in humans. © 2015 by the authors; licensee MDPI, Basel, Switzerland.


Egger L.,Institute for Food science | Nicolas M.,National Reference Laboratory for Milk and Milk Products EURL | Pellegrino L.,University of Milan
LWT - Food Science and Technology | Year: 2016

Alkaline phosphatase (ALP) activity is used throughout the world as a marker for the proper pasteurization of milk, to guarantee its hygienic safety. The Standard ISO 11816-2/IDF 155-2 describes the analysis of ALP in cheese. However, the method has been questioned in the past because there have sometimes been ambiguous results. The critical operations of the analytical procedure are more precisely defined and a zonal cheese sampling adopted. ALP inactivation is firstly evaluated in the relevant steps of controlled cheese makings of hard (Emmental), semi-hard (Raschera) and soft (Chaource) cheeses. Application of the improved procedure in over 700 samples of typical cheeses from France, Italy and Switzerland proved the applicability of the method. Based on this large study, a limit for ALP activity in cheese from pasteurized milk is proposed at 10 mU/g. © 2015 The Authors.


Gekenidis M.-T.,Institute for Food science | Studer P.,Institute for Food science | Studer P.,ETH Zurich | Wuthrich S.,ETH Zurich | And 2 more authors.
Applied and Environmental Microbiology | Year: 2014

A well-accepted method for identification of microorganisms uses matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) coupled to analysis software which identifies and classifies the organism according to its ribosomal protein spectral profile. The method, called MALDI biotyping, is widely used in clinical diagnostics and has partly replaced conventional microbiological techniques such as biochemical identification due to its shorter time to result (minutes for MALDI biotyping versus hours or days for classical phenotypic or genotypic identification). Besides its utility for identifying bacteria, MS-based identification has been shown to be applicable also to yeasts and molds. A limitation to this method, however, is that accurate identification is most reliably achieved on the species level on the basis of reference mass spectra, making further phylogenetic classification unreliable. Here, it is shown that combining tryptic digestion of the acid/organic solvent extracted (classical biotyping preparation) and resolubilized proteins, nano-liquid chromatography (nano-LC), and subsequent identification of the peptides by MALDI-tandem TOF (MALDI-TOF/TOF) mass spectrometry increases the discrimination power to the level of subspecies. As a proof of concept, using this targeted proteomics workflow, we have identified subspeciesspecific biomarker peptides for three Salmonella subspecies, resulting in an extension of the mass range and type of proteins investigated compared to classical MALDI biotyping. This method therefore offers rapid and cost-effective identification and classification of microorganisms at a deeper taxonomic level. © 2014, American Society for Microbiology.


PubMed | Institute for Food science, ETH Zurich and University of Bern
Type: | Journal: Preventive veterinary medicine | Year: 2016

Staphylococcus aureus is a common mastitis causing pathogen of dairy cattle. Several S. aureus genotypes exist, of which genotype B (GTB) is highly prevalent in Swiss dairy herds. Dairy farming in mountainous regions of Switzerland is characterised by the movement of dairy cattle to communal pasture-based operations at higher altitudes. Cows from different herds of origin share pastures and milking equipment for a period of 2 to 3 months during summer. The aim of this longitudinal observational study was to quantify transmission of S. aureus GTB in communal dairy operations. Cows (n=551) belonging to 7 communal operations were sampled at the beginning and end of the communal period. Transmission parameter was estimated using a Susceptible-Infectious-Susceptible (SIS) model. The basic reproduction ratio R


Gasser F.,Institute for Food science | Von Arx K.,Institute for Food science
Acta Horticulturae | Year: 2015

Two new tools for improved preservation of apple quality have been developed in recent years: the treatment of apples with 1-MCP (trade name SmartFresh™) and the dynamic controlled atmosphere storage (DCA). Because of the nature of the treatment, 1-MCP may not be applied for organically grown apples, whereas DCA may be used for organic fruit. Over three years, selected hotwater treated and non-treated organic apple cultivars ('Topaz', 'Ariane', 'Otava') were stored under DCA-conditions in order to examine whether hot water treatment has an impact on fruit stress during DCA-storage and if DCA-stored fruit retain quality better than ULO-stored fruit during long-term storage. Furthermore, organic fruit were compared to fruit produced under "integrated production" conditions (IP). The critical oxygen concentration (anaerobic compensation point, ACP) during DCA-storage was not influenced by previous hot-water treatment nor by the production method. However, ACP varied from year to year (e.g., for 'Topaz' 0.20, 0.18 and 0.56 kPa O2 over 3 years), showing that yearly fluctuations of climatic conditions during production may influence fruit behaviour during storage. For 'Topaz' and 'Otava', DCA had no positive effect on fruit quality compared to ULO conditions, whereas for 'Ariane', DCA stored fruit retained fruit firmness and acidity better compared to fruit stored under ULO conditions. Hot-water treatment did not affect fruit quality and the incidence of physiological disorders of DCAstored apple. Fruit rot was affected by the cultivar, 'Topaz' being the most susceptible cultivar and 'Ariane' the most resistant to fruit rot. Organic fruit were susceptible to higher fruit rot during DCA-storage than IP fruit. Compared to ULO conditions, DCA did not reduce fruit rot.


Gille D.,Institute for Food science | Schmid A.,Institute for Food science
Nutrition Reviews | Year: 2015

Vitamin B12 is synthesized exclusively by microorganisms; therefore, humans must absorb it from food. Excellent sources of B12 are foods of ruminant origin, so dairy and meat products play an important role in efforts to meet the official daily B12 intake recommendation of 3.0 μg. Concentrations of the vitamin vary within foods of ruminant origin, with the highest concentrations found in offal such as liver and kidney. In comparison, dairy products have much lower quantities of the vitamin. In bovine milk, the B12 concentration is stable with regard to breed, feed, season, and stage of lactation, but in ruminant meat, the amount of B12 can vary based on the feeding and husbandry of the animal as well as the cut of meat chosen and its preparation. Processing of ruminant food, including thermal treatment, usually diminishes the vitamin B12 concentration. This review summarizes the vitamin B12 content of foods and discusses the impact of food processing on vitamin content. The contribution of ruminant food sources to B12 intake is specifically evaluated, with its bioavailability taken into account. © The Author(s) 2015.

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