In vitro and in planta fungicide properties of ozonated water against the esca-associated fungus Phaeoacremonium aleophilum

Ozone could be used as a sanitary agent in the food and agricultural industries. The present study investigates whether ozonated water could be used to control conidia dispersal of the esca-associated fungus Phaeoacremonium aleophilum. The fungicide properties of ozonated water was firstly assessed in vitro by exposing spores to several concentrations of ozonated water (2.2, 4.5, or 13.5g/m3 of ozone dissolved into water) and observing the germination rate on plate. Secondarily an in planta approach was conducted on grapevine cuttings of cv. Cabernet Sauvignon clone 15. P. aleophilum conidia were inoculated in pruning wounds, which then received ozonated (4.5g/m3) or sterile water. P. aleophilum DNA was quantified by a quantitative polymerase chain reaction (qPCR) 4 and 9 weeks post-inoculation. The effect of ozonated water on plant-defense gene expression was monitored by reverse-transcriptase qPCR (RT-qPCR) 48h post treatment. The results indicate that ozonated water totally suppresses spore germination in vitro. In addition, at 9 weeks post-inoculation, fungal development was significantly reduced by 50% in planta. RT-qPCR analysis shows that ozonated water did not induce plant-defense-related genes 48h post treatment. The fungicide properties of ozonated water and the absence of gene induction in planta make however ozonated water a promising candidate for limiting grapevine infection by P. aleophilum in nurseries

Discrimination of lactic acid bacteria Enterococcus and Lactococcus by infrared spectroscopy and multivariate techniques

Raw milk is often described as a major source of lactic acid bacteria for indigenous lactic starter. These indigenous starters contribute to the sensorial quality of cheese. Raw milk, rich in Lactoccocus lactis may therefore be very interesting for the cheese making. Currently, the most commonly used methods to differentiate lactic acid bacteria, and particularly the closely related phenotypes Lactococcus and Enterococcus, are based on DNA sequencing, but the cost and time required for these analytical methods hinder their use for rapid screening of raw material. The present study therefore proposes a simple alternative method to identify and discriminate against Lactococcus and Enterococcus, at the genus, but also at the species level, that is based on collecting near infrared spectra directly from bacterial colonies in Petri dishes. The infrared spectra of 280 strains of Lactococcus and Enterococcus cultured on solid media were collected by using a spectrometer with a wavelength range of 908 to 1684 nm and a remote probe. The best Classification And Regression Trees models for genus and species discrimination gave an excellent classification rate of 87% on an external validation set (30 strains). Loading line plots, with prominent bands at 900–960 and 1270–1390 nm, confirmed that the source of variation was due to changes in the polysaccharides

Complete exon sequencing of all known Usher syndrome genes greatly improves molecular diagnosis

<p>Abstract</p> <p>Background</p> <p>Usher syndrome (USH) combines sensorineural deafness with blindness. It is inherited in an autosomal recessive mode. Early diagnosis is critical for adapted educational and patient management choices, and for genetic counseling. To date, nine causative genes have been identified for the three clinical subtypes (USH1, USH2 and USH3). Current diagnostic strategies make use of a genotyping microarray that is based on the previously reported mutations. The purpose of this study was to design a more accurate molecular diagnosis tool.</p> <p>Methods</p> <p>We sequenced the 366 coding exons and flanking regions of the nine known USH genes, in 54 USH patients (27 USH1, 21 USH2 and 6 USH3).</p> <p>Results</p> <p>Biallelic mutations were detected in 39 patients (72%) and monoallelic mutations in an additional 10 patients (18.5%). In addition to biallelic mutations in one of the USH genes, presumably pathogenic mutations in another USH gene were detected in seven patients (13%), and another patient carried monoallelic mutations in three different USH genes. Notably, none of the USH3 patients carried detectable mutations in the only known USH3 gene, whereas they all carried mutations in USH2 genes. Most importantly, the currently used microarray would have detected only 30 of the 81 different mutations that we found, of which 39 (48%) were novel.</p> <p>Conclusions</p> <p>Based on these results, complete exon sequencing of the currently known USH genes stands as a definite improvement for molecular diagnosis of this disease, which is of utmost importance in the perspective of gene therapy.</p

From genome to phenotype: An integrative approach to evaluate the biodiversity of Lactococcus lactis

Lactococcus lactis is one of the most extensively used lactic acid bacteria for the manufacture of dairy products. Exploring the biodiversity of L. lactis is extremely promising both to acquire new knowledge and for food and health-driven applications. L. lactis is divided into four subspecies: lactis, cremoris, hordniae and tructae, but only subsp. lactis and subsp. cremoris are of industrial interest. Due to its various biotopes, Lactococcus subsp. lactis is considered the most diverse. The diversity of L. lactis subsp. lactis has been assessed at genetic, genomic and phenotypic levels. Multi-Locus Sequence Type (MLST) analysis of strains from different origins revealed that the subsp. lactis can be classified in two groups: “domesticated” strains with low genetic diversity, and “environmental” strains that are the main contributors of the genetic diversity of the subsp. lactis. As expected, the phenotype investigation of L. lactis strains reported here revealed highly diverse carbohydrate metabolism, especially in plant- and gut-derived carbohydrates, diacetyl production and stress survival. The integration of genotypic and phenotypic studies could improve the relevance of screening culture collections for the selection of strains dedicated to specific functions and applications

Identification of lactic acid bacteria and rhizobacteria by ultraviolet-visible-near infrared spectroscopy and multivariate classification

International audienceThe biological processes of interest to agro-industry involve numerous bacterial species. Lactic acid bacteria produce metabolites capable of fermenting food products and modifying their organoleptic properties, and plant-growth-promoting rhizobacteria can act as biofertilizers, biostimulants, or biocontrol agents in agriculture. The protocol of conventional techniques for bacterial identification, currently based on genotyping and phenotyping, require specific sample preparation and destruction. The work presented herein details a method for rapid identification of lactic acid bacteria and rhizobacteria at the genus and species level. To develop the method, bacteria were inoculated on an agar medium and analyzed by near infrared (NIR) and ultraviolet-visible-NIR (UV-Vis-NIR) spectroscopy. Artificial neural network models applied to the UV-Vis-NIR spectra correctly identified the genus (species) of 70% (63%) of the lactic acid bacteria and 67% of the rhizobacteria on an independent prediction set of unknown bacterial strains. These results demonstrate the potential of UV-Vis-NIR spectroscopy to identify bacteria directly on agar plates

Harnessing diversity of Lactococcus lactis from raw goat milk: Design of an indigenous starter for the production of Rocamadour, a French PDO cheese

International audienceThe single cell protein (SCP) technique has become a popular technology in recent days, which addresses two major issues: increasing world protein deficiency with increasing world population and the generation of substantial industrial wastes with an increased production rate. Global fruit production has increased over the decades. The non-edible parts of fruits are discarded as wastes into the environment, which may result in severe environmental issues. These fruit wastes are rich in fermentable sugars and other essential nutrients, which can be effectively utilized by microorganisms as an energy source to produce microbial protein. Taking this into consideration, this review explores the use of fruit wastes as a substrate for SCP production. Many studies reported that the wastes from various fruits such as orange, sweet orange, mango, banana, pomegranate, pineapple, grapes, watermelon, papaya, and many others are potential substrates for SCP production. These SCPs can be used as a protein supplement in human foods or animal feeds. This paper discusses various aspects in regard to the potential of fruit wastes as a substrate for SCP production

Artisanal Household Milk Pasteurization Is Not a Determining Factor in Structuring the Microbial Communities of Labneh Ambaris: A Pilot Study

Labneh Ambaris is a traditional Lebanese dairy product traditionally made using raw goat’s milk in earthenware jars, but recently the use of artisanally pasteurized milk was introduced for safety reasons. In this study, 12 samples of labneh Ambaris were studied, six made using raw goat’s milk and six others using artisanally pasteurized goat’s milk. These samples were collected during fermentation and their microbial compositions were analyzed. The 16S V3–V4 and the ITS2 regions of the rDNA were sequenced by DNA metabarcoding analyses for the identification and comparison of bacterial and fungal communities, respectively. The samples had high microbial diversity but differences in samples microbiota were unrelated to whether or not milk was pasteurized. The samples were consequently clustered on the basis of their dominant bacterial or fungal species, regardless of the milk used. Concerning bacterial communities, samples were clustered into 3 groups, one with a higher abundance of Lactobacillus helveticus, another with Lactobacillus kefiranofaciens as the dominant bacterial species, and the third with Lentilactobacillus sp. as the most abundant species. Species belonging to the Enterobacteriaceae family were detected in higher abundance in all raw milk samples than in artisanally pasteurized milk samples. As for fungal communities, the samples were clustered into two groups, one dominated by Geotrichum candidum and the other by Pichia kudriavzevii

Microbial communities and main features of labneh Ambaris, a traditional Lebanese fermented goat milk product

ABSTRACT: Labneh Ambaris is a traditional Lebanese dairy product typically made using goat milk in special earthenware jars. Its production is characterized by the regular additions of milk and coarse salt, all while draining the whey throughout a process that lasts for a minimum of 2 mo. In this study, 20 samples of labneh Ambaris, all produced by spontaneous fermentation, were studied. They were collected at the end of fermentation from different regions in Lebanon. Physicochemical and sensory properties were studied and microbial diversity was analyzed using culture-dependent and independent techniques. The V3–V4 region of the 16S rRNA gene and the ITS2 region were sequenced by DNA metabarcoding analyses for the identification of bacteria and yeast communities, respectively. Out of 160 bacterial and 36 fungal taxa, 117 different bacterial species and 24 fungal species were identified among all labneh Ambaris samples studied. The remaining ones were multi-affiliated and could not be identified at the species level. Lactobacillus was the dominant bacterial genus, followed by Lentilactobacillus, Lactiplantibacillus, Lacticaseibacillus, and Lactococcus genera, whereas Geotrichum and Pichia were the dominant fungal genera. The 20 samples tested had varying levels of salt, protein, and fat contents, but they were all highly acidic (mostly having a pH < 4). According to the sensory scores generated by classical descriptive analysis, all samples were described as having basic similar characteristics such as goat smell and flavor, but they could be differentiated based on various intensities within the same descriptors like salty and acidic. This work could be considered as a base toward obtaining a quality label for labneh Ambaris

5000 ans d’histoire sous la Méridienne. Les fouilles de l’A75 au sud de Clermont-Ferrand

International audienceDe remarquables ensembles funéraires préhistoriques et protohistoriques, des alignements de menhirs associés à une inédite stèle féminine datant du Néolithique... Les fouilles effectuées sur plus de 13 kilomètres au sud et à l'est de Clermont-Ferrand et liées à la mise à 2 x 3 voies de l'autoroute A75 ont permis la découverte de vestiges exceptionnels. Démontrant tout son intérêt scientifique et patrimonial, l'archéologie préventive révèle une occupation humaine longue, continue et d'une rare densité sur cet axe méridien au cours des cinq millénaires avant notre ère : depuis la Préhistoire jusqu'à la fin de l'indépendance gauloise, la région s'avère un carrefour majeur entre l'Europe continentale et la Méditerranée. Ce bel ouvrage est l'édifiant carnet de voyage des archéologues lancés sur les traces des Arvernes et des premières populations sédentaires qui les ont précédés à partir du début du Néolithique, il y a 7000 ans