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Independent domestication events in the blue-cheese fungus Penicillium roqueforti
No full textDomestication provides an excellent framework for studying adaptive divergence. Using population genomics and phenotypic assays, we reconstructed the domestication history of the blue cheese mold Penicillium roqueforti. We showed that this fungus was domesticated twice independently. The population used in Roquefort originated from an old domestication event associated with weak bottlenecks and exhibited traits beneficial for pre-industrial cheese production (slower growth in cheese and greater spore production on bread, the traditional multiplication medium). The other cheese population originated more recently from the selection of a single clonal lineage, was associated to all types of blue cheese worldwide but Roquefort, and displayed phenotypes more suited for industrial cheese production (high lipolytic activity, efficient cheese cavity colonization ability and salt tolerance). We detected genomic regions affected by recent positive selection and putative horizontal gene transfers. This study sheds light on the processes of rapid adaptation and raises questions about genetic resource conservation
FROM’MIR : Développer des outils de prédiction et de conseil pour maîtriser la fromageabilité des laits destinés à la fabrication des fromages traditionnels franc-comtois
No full textDes équations MIR (spectrométrie moyen infrarouge) d'estimation de la fromageabilité des laits,
établies en contexte AOP/IGP franc-comtois, existent pour la première fois en France. Le rendement
laboratoire extrait sec (ES), cohérent avec les rendements observés en mini-fabrications de fromages à
pâte molle et à pâte pressée cuite, est le paramètre le mieux prédit. Dans nos conditions, certains
aspects de l'aptitude à la coagulation enzymatique, comme la fermeté des gels, peuvent être estimés.
L’aptitude à l’acidification, dépendant fortement de la composante microbiologique des laits, est quant à
elle mal estimée. Les meilleures performances de prédiction sont obtenues sur les laits individuels de
vaches. Les performances sont moins bonnes à l’échelle des laits de mélange, des laits de troupeaux
mais surtout des laits de cuves de fromagerie. L'étude des facteurs de variation a permis de mettre en
évidence le poids important de la génétique avec un niveau d’héritabilité élevé et des effets forts des
régions du génome impliquées. La qualité et la quantité de fourrages ainsi que la répartition des
vêlages sont influents dans le contexte étudié. Dans ce même contexte, peu de facteurs de variation
ont été mis en évidence à l’échelle des laits de cuves, les pratiques étant très encadrées par le cahier
des charges AOP. A l’issue de ce projet, un observatoire, depuis la qualité des laits jusqu’à celle des
fromages, va être mis en place en Franche Comté. Des études seront aussi mises en œuvre au niveau
national pour permettre notamment une consolidation et une amélioration des équations dans d'autres
contextes.Mid-infrared spectroscopy prediction equations of the cheese-making properties of milk, established in
the Franche-Comté PDO/PGI context, exist for the first time in France. Laboratory curd yield in Dry
Matter was consistent with the yields observed in mini-manufactures of soft and pressed cooked
cheeses and it is the best predicted parameter. Under our conditions, some coagulation properties such
as curd firmness could be estimated. The acidification properties, which heavily depend on the
microbiological component of milk, are poorly estimated. The best prediction performances were
obtained on individual cow milks. The performances were poorer on the scale of bulk milks, herd tank
milk but especially dairy vat milk. The study of variation factors made it possible to highlight the
important weight of genetics with a high level of heritability and strong effects of the genome regions
involved. The quality and quantity of fodder and the distribution of calves were influential in the context
studied. In this same context, few factors of variation have been identified at the scale of dairy vat milks,
as the practices were very much governed by the PDO specifications. At the end of this project, an
observatory, from the quality of the milk to the quality of the cheese, will be set up in Franche Comté.
Studies will also be carried out at the national level to consolidate and improve the equations in other
contexts
L'agriculture comme nature en ville ? Le cas de l'Agriparc du Mas Nouguier, Montpellier, France
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Diverse and variable virus communities in wild plant populations revealed by metagenomic tools
No full textWild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Aland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild
How to prevent viremia rebound? Evidence from a PRRSv data-supported model of immune response
No full textBackground[br/]
Understanding what determines the between-host variability in infection dynamics is a key issue to better control the infection spread. In particular, pathogen clearance is desirable over rebounds for the health of the infected individual and its contact group. In this context, the Porcine Respiratory and Reproductive Syndrome virus (PRRSv) is of particular interest. Numerous studies have shown that pigs similarly infected with this highly ubiquitous virus elicit diverse response profiles. Whilst some manage to clear the virus within a few weeks, others experience prolonged infection with a rebound. Despite much speculation, the underlying mechanisms responsible for this undesirable rebound phenomenon remain unclear.
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Results[br/]
We aimed at identifying immune mechanisms that can reproduce and explain the rebound patterns observed in PRRSv infection using a mathematical modelling approach of the within-host dynamics. As diverse mechanisms were found to influence PRRSv infection, we established a model that details the major mechanisms and their regulations at the between-cell scale. We developed an ABC-like optimisation method to fit our model to an extensive set of experimental data, consisting of non-rebounder and rebounder viremia profiles. We compared, between both profiles, the estimated parameter values, the resulting immune dynamics and the efficacies of the underlying immune mechanisms. Exploring the influence of these mechanisms, we showed that rebound was promoted by high apoptosis, high cell infection and low cytolysis by Cytotoxic T Lymphocytes, while increasing neutralisation was very efficient to prevent rebounds.
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Conclusions[br/]
Our paper provides an original model of the immune response and an appropriate systematic fitting method, whose interest extends beyond PRRS infection. It gives the first mechanistic explanation for emergence of rebounds during PRRSv infection. Moreover, results suggest that vaccines or genetic selection promoting strong neutralising and cytolytic responses, ideally associated with low apoptotic activity and cell permissiveness, would prevent rebound
Volatolomics in bacterial ecotoxicology, A novel method for detecting signatures of pesticide exposure?
No full textVolatile organic compounds (VOC) produced by microorganisms in response
to chemical stressor showed recently increasing attention, because of possible
environmental applications. In this work, we aimed to bring the first proof of concept
that volatolomic (i.e., VOCs analysis) can be used to determine candidate VOC
markers of two soil bacteria strains (Pseudomonas fluorescens SG-1 and Bacillus
megaterium Mes11) exposure to pesticides. VOC determination was based on solidphase
microextraction (SPME) coupled with gas chromatography-mass spectrometry
(GC-MS). Accordingly, we highlighted a set of bacterial VOCs modulated in each
strains according to the nature of the pesticide used. Three out these VOCs were
specifically modulated in P. fluorescens SG-1 when exposed with two pyrethroid
pesticides (deltamethrine and cypermethrine): 2-hexanone; 1,3-ditertbutylbenzene and
malonic acid, hexyl 3-methylbutyl ester. Our results thus suggest the possible existence
of generic VOC markers of pyrethroids in this strain. Of particular interest, two out of
these three VOCs, the 1,3-ditertbutylbenzene and the malonic acid, hexyl 3-methylbutyl
ester were found also in B. megaterium Mes11 when exposed with cypermethrine.
This result highlighted the possible existence of interspecific VOC markers of pyrethroid
in these two bacteria. Altogether, our work underlined the relevance of volatolomic
to detect signatures of pesticides exposure in microorganisms and more generally to
microbial ecotoxicology. Based on these first results, considerations of volatolomics for
the chemical risk assessment in environment such as soils can be indirectly explored in
longer terms
Nutrimetabolomics: An integrative action for metabolomic analyses in human nutritional studies
No full textThe life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance (funded by the European Joint Programming Initiative "A Healthy Diet for a Healthy Life" (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but rather to present a pragmatic guidance on metabolomic methodologies, providing readers with useful "tips and tricks" along the analytical workflow
Cerebral gustatory activation in response to free fatty acids using gustatory evoked potentials in humans
No full textThere is some evidence of specific oro-detection of free fatty acids (FFA) in rodents and humans. The aim of this study was to record gustatory evoked potentials (GEPs) in response to FFA solutions, and to compare GEPs in response to linoleic acid solution with GEPs obtained after stimulation with sweet and salty tastants. Eighteen healthy men were randomly stimulated with fatty (linoleic acid), sweet (sucrose) and salty (NaCl) solutions, at two concentrations in the first experiment. Control recordings (n=14) were obtained during stimulation by a paraffin oil mixture without FFA or by water. In the second experiment, eighteen men were randomly stimulated with 5 FFA solutions and a paraffine emulsion. GEPs were recorded with EEG electrodes at Cz, Fz, Pz. GEPs were observed in response to FFA in all participants. GEP characteristics did not differ according to the quality and the concentration of the solutions in the first experiment, and according to the FFA in the second experiment. This study described for the first time GEPs in response to FFA and demonstrated that the presence of FFA in mouth triggers an activation of the gustatory cortex. These data reinforce the concept that fat taste could be the sixth primary taste
Milk fat composition modifies the texture and appearance of Cantal-type cheeses but not their flavor
No full textAlthough the effects of cow diet on cheese sensory properties have been well documented, the putative interactions between the biochemical and microbial milk components and their respective roles in the development of the sensory properties of cheeses have yet to be explored in depth. The aim of this study was to evaluate the specific contribution of milk fat composition to the formation of cheese sensory properties. Two creams with different fat compositions were obtained from cows fed either pasture or maize silage. Cheeses were manufactured from the same skim milk (identical chemical and microbial composition) with either the pasture- or maize silage-origin pasteurized cream added. The gross composition and microbial composition of milks did not vary with cream origin. In milks and cheeses, the fatty acid (FA) profiles were modified by the origin of the cream. The concentrations of C18:0 and unsaturated FA such as cis-9 C18:1, trans-11 C18:1, C18:3n-3, total conjugated linoleic acids, and mono- and polyunsaturated FA were higher in milks and cheeses with the pasture-origin cream than in those with the maize-origin cream. In contrast, the maize milks and cheeses had higher concentrations of short- and medium-chain saturated FA, C16:0, and C18:2n-6. The level of lipolysis was 11% in the cheese rind and only 0.30% in the cheese core. The rind of pasture cheeses had a higher concentration of free C18:0 and C18:3n-3 and a lower concentration of free C14:0 and free C16:0 than the rind of maize cheeses. The levels of major microbial groups were similar in pasture and maize cheeses at different stages of ripening. The pasture cheeses had a more elastic and creamier texture, a yellower color, and a thinner rind than the maize cheeses, but the odor and aroma of cheeses were not affected by the origin of the cream, despite a few modifications in the balance of volatile compounds from FA catabolism. Based on these results, we conclude that milk fat composition modulated by cow diet had a direct role in the texture of the cheese but no effect on flavor. The high degree of lipolysis in cheese rind, along with the higher concentration of long-chain unsaturated free FA in pasture cheeses may be responsible for antimicrobial activity, which could explain differences in the appearance of cheese rind