Publications by authors named "Philippe Ruiz"

7 Publications

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Changes in Digestive Microbiota, Rumen Fermentations and Oxidative Stress around Parturition Are Alleviated by Live Yeast Feed Supplementation to Gestating Ewes.

J Fungi (Basel) 2021 Jun 4;7(6). Epub 2021 Jun 4.

Lallemand SAS, 19 rue des Briquetiers, BP 59, CEDEX, 31702 Blagnac, France.

Background: In ruminants, physiological and nutritional changes occur peripartum. We investigated if gastro-intestinal microbiota, rumen metabolism and antioxidant status were affected around parturition and what could be the impact of a daily supplementation of a live yeast additive in late gestating ewes.

Methods: Rumen, feces and blood samples were collected from 2 groups of 14 ewes one month and a few days before parturition, and 2 weeks postpartum.

Results: In the control ewes close to parturition, slight changes in the ruminal microbiota were observed, with a decrease in the concentration and in the relative abundance of the Fibrobacteres phylum. Moreover, a decrease in the alpha-diversity of the bacterial community and a reduced relative abundance of the Fibrobacteres phylum were observed in their feces. Control ewes were prone to oxidative stress, as shown by an increase in malondialdehyde (MDA) concentration, a lower total antioxidant status, and higher glutathione peroxidase (GPx) activity in the blood. In the yeast supplemented ewes, most of the microbial changes observed in the control group were alleviated. An increase in GPx activity, and a significant decrease in MDA concentration were measured.

Conclusions: The live yeast used in this study could stabilize gastro-intestinal microbiota and reduce oxidative stress close to parturition.
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http://dx.doi.org/10.3390/jof7060447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8228133PMC
June 2021

Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses.

mBio 2021 03 3;12(2). Epub 2021 Mar 3.

Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Clermont-Ferrand, France

, , and are the three predominant cellulolytic bacterial species found in the rumen. studies have shown that these species compete for adherence to, and growth upon, cellulosic biomass. Yet their molecular interactions have not heretofore been examined. Gnotobiotically raised lambs harboring a 17-h-old immature microbiota devoid of culturable cellulolytic bacteria and methanogens were inoculated first with S85 and sp. strain 87.7, and 5 months later, the lambs were inoculated with 8 and FD-1. Longitudinal samples were collected and profiled for population dynamics, gene expression, fibrolytic enzyme activity, fibrolysis, and metabolite profiling. Quantitative PCR, metagenome and metatranscriptome data show that establishes at high levels initially but is gradually outcompeted following the introduction of the ruminococci. This shift resulted in an increase in carboxymethyl cellulase (CMCase) and xylanase activities but not in greater fibrolysis, suggesting that and ruminococci deploy different but equally effective means to degrade plant cell walls. Expression profiles showed that relied upon outer membrane vesicles and a diverse repertoire of CAZymes, while and preferred type IV pili and either CBM37-harboring or cellulosomal carbohydrate-active enzymes (CAZymes), respectively. The changes in cellulolytics also affected the rumen metabolome, including an increase in acetate and butyrate at the expense of propionate. In conclusion, this study provides the first demonstration of competition between the three predominant cellulolytic bacteria and provides insight on the influence of these ecological interactions on rumen fibrolytic function and metabolomic response. Ruminant animals, including cattle and sheep, depend on their rumen microbiota to digest plant biomass and convert it into absorbable energy. Considering that the extent of meat and milk production depends on the efficiency of the microbiota to deconstruct plant cell walls, the functionality of predominant rumen cellulolytic bacteria, , , and , has been extensively studied to obtain a better knowledge of how they operate to hydrolyze polysaccharides and ultimately find ways to enhance animal production. This study provides the first evidence of competitions between and the two species. It shows that a simple disequilibrium within the cellulolytic community has repercussions on the rumen metabolome and fermentation end products. This finding will have to be considered in the future when determining strategies aiming at directing rumen fermentations for animal production.
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http://dx.doi.org/10.1128/mBio.03533-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8092306PMC
March 2021

Physicochemical and microbiological characteristics of El-Guedid from meat of different animal species.

Meat Sci 2021 Jan 11;171:108277. Epub 2020 Aug 11.

Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand 63000, France.

El-Guedid is an Algerian traditional meat-based product that is prepared from red meats. It belongs to the wide diversity of salted/dried meat products. This study described the physicochemical and microbiological properties of different products from four animal origins and during all the conservation. Results indicated that these products were mainly characterized by a low moisture with an average decrease of water content between 15.6% and 16.3% for all the samples, and a decrease in water activity ranging from 0.66 to 0.68, while the salt content ranged from 8.8 to 19.3%. A decrease in pH values oscillated from (6.3-6.4) to reach (5.2-5.5) at T0 and T365 consecutively, in all the samples. Microbial analyses revealed the absence of pathogenic bacteria such as Listeria and Salmonella but the sporadic contamination by Staphylococcus aureus up to one month of ripening. Lactic acid bacteria and coagulase negative staphylococci were the dominant populations in El-Guedid with Leuconostoc mesenteroides, Lactobacillus sakei, and Staphylococcus saprophyticus as the main species identified. All these populations decreased along the process and reached low levels (2 log CFU/g) at the end of storage (365 days). The drastic drying of El-Guedid led to safe traditional meat product that could promote its production.
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http://dx.doi.org/10.1016/j.meatsci.2020.108277DOI Listing
January 2021

Differential homotypic and heterotypic interactions of antigen 43 (Ag43) variants in autotransporter-mediated bacterial autoaggregation.

Sci Rep 2019 07 31;9(1):11100. Epub 2019 Jul 31.

Université Clermont Auvergne, INRA, UMR454 MEDiS, 63000, Clermont-Ferrand, France.

Antigen 43 (Ag43) is a cell-surface exposed protein of Escherichia coli secreted by the Type V, subtype a, secretion system (T5aSS) and belonging to the family of self-associating autotransporters (SAATs). These modular proteins, comprising a cleavable N-terminal signal peptide, a surface-exposed central passenger and an outer membrane C-terminal translocator, self-recognise in a Velcro-like handshake mechanism. A phylogenetic network analysis focusing on the passenger revealed for the first time that they actually distribute into four distinct classes, namely C1, C2, C3 and C4. Structural alignment and modelling analyses demonstrated these classes arose from shuffling of two different subdomains within the Ag43 passengers. Functional analyses revealed that homotypic interactions occur for all Ag43 classes but significant differences in the sedimentation kinetics and aggregation state were present when Ag43 was expressed. In contrast, heterotypic interaction occurred in a very limited number of cases. Single cell-force spectroscopy demonstrated the importance of specific as well as nonspecific interactions in mediating Ag43-Ag43 recognition. We propose that structural differences in the subdomains of the Ag43 classes account for different autoaggregation dynamics and propensities to co-interact.
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http://dx.doi.org/10.1038/s41598-019-47608-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6668479PMC
July 2019

Procyanidin-Cell Wall Interactions within Apple Matrices Decrease the Metabolization of Procyanidins by the Human Gut Microbiota and the Anti-Inflammatory Effect of the Resulting Microbial Metabolome In Vitro.

Nutrients 2019 Mar 19;11(3). Epub 2019 Mar 19.

Université Clermont Auvergne, INRA, UMR 0454 MEDIS, F-63000 Clermont-Ferrand, France.

B-type oligomeric procyanidins in apples constitute an important source of polyphenols in the human diet. Their role in health is not known, although it is suggested that they generate beneficial bioactive compounds upon metabolization by the gut microbiota. During apple processing, procyanidins interact with cell-wall polysaccharides and form stable complexes. These interactions need to be taken into consideration in order to better assess the biological effects of fruit constituents. Our objectives were to evaluate the impact of these interactions on the microbial metabolization of cell walls and procyanidins, and to investigate the potential anti-inflammatory activity of the resulting metabolome, in addition to analyzing the taxonomical changes which the microbiota undergo. In vitro fermentation of three model apple matrices with microbiota from 4 healthy donors showed that the binding of procyanidins to cell-wall polysaccharides, whether covalently or non-covalently, substantially reduced procyanidin degradation. Although cell wall-unbound procyanidins negatively affected carbohydrate fermentation, they generated more hydroxyphenylvaleric acid than bound procyanidins, and increased the abundance of and genera. The best results in terms of production of anti-inflammatory bioactive metabolites were observed from the apple matrix with no bonds between procyanidins and cell wall polysaccharides, although the matrix with non-covalent bonds was not far behind.
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http://dx.doi.org/10.3390/nu11030664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6471247PMC
March 2019

Robust Fit of Toxicokinetic-Toxicodynamic Models Using Prior Knowledge Contained in the Design of Survival Toxicity Tests.

Environ Sci Technol 2017 04 22;51(7):4038-4045. Epub 2017 Mar 22.

Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558 , Laboratoire de Biométrie et Biologie Évolutive, F-69622, Villeurbanne, France.

Toxicokinetics-toxicodynamic (TKTD) models have emerged as a powerful means to describe survival as a function of time and concentration in ecotoxicology. They are especially powerful to extrapolate survival observed under constant exposure conditions to survival predicted under realistic fluctuating exposure conditions. But despite their obvious benefits, these models have not yet been adopted as a standard to analyze data of survival toxicity tests. Instead simple dose-response models are still often used although they only exploit data observed at the end of the experiment. We believe a reason precluding a wider adoption of TKTD models is that available software still requires strong expertise in model fitting. In this work, we propose a fully automated fitting procedure that extracts prior knowledge on parameters of the model from the design of the toxicity test (tested concentrations and observation times). We evaluated our procedure on three experimental and 300 simulated data sets and showed that it provides robust fits of the model, both in the frequentist and the Bayesian framework, with a better robustness of the Bayesian approach for the sparsest data sets.
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http://dx.doi.org/10.1021/acs.est.6b05326DOI Listing
April 2017

Measuring fluid intelligence on a ratio scale: evidence from nonverbal classification problems and information entropy.

Authors:
Philippe E Ruiz

Behav Res Methods 2009 May;41(2):439-45

ESC Lille Graduate School-LSMRC, Euralille, France.

Drawing on the g factor and information theory literatures, the relationship between the four subtests of the Culture-Fair Intelligence Test (CFIT) and the entropy of the Ruiz Absolute Scale of Complexity Management (R-ASCM) was investigated. In results based on data collected from 186 university students, the entropy of the R-ASCM mostly loads the first principal component extracted from the CFIT subtests and shows a corresponding strong relationship with the item difficulty of the R-ASCM. Because entropy is a ratio scale of complexity--with a true zero and units called bits--these findings suggest that entropy is the right vehicle for measuring the information contained in nonverbal intelligence tests.
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http://dx.doi.org/10.3758/BRM.41.2.439DOI Listing
May 2009
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