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Dive into the research topics where Mahendra Mariadassou is active.

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Featured researches published by Mahendra Mariadassou.


Environmental Microbiology | 2016

Beneficial metabolic effects of selected probiotics on diet‐induced obesity and insulin resistance in mice are associated with improvement of dysbiotic gut microbiota

Jeanne Alard; Véronique Lehrter; Moez Rhimi; Irène Mangin; Véronique Peucelle; Anne-Laure Abraham; Mahendra Mariadassou; Emmanuelle Maguin; Anne-Judith Waligora-Dupriet; Bruno Pot; Isabelle Wolowczuk; Corinne Grangette

Alterations in gut microbiota composition and diversity were suggested to play a role in the development of obesity, a chronic subclinical inflammatory condition. We here evaluated the impact of oral consumption of a monostrain or multi-strain probiotic preparation in high-fat diet-induced obese mice. We observed a strain-specific effect and reported dissociation between the capacity of probiotics to dampen adipose tissue inflammation and to limit body weight gain. A multi-strain mixture was able to improve adiposity, insulin resistance and dyslipidemia through adipose tissue immune cell-remodelling, mainly affecting macrophages. At the gut level, the mixture modified the uptake of fatty acids and restored the expression level of the short-chain fatty acid receptor GPR43. These beneficial effects were associated with changes in the microbiota composition, such as the restoration of the abundance of Akkermansia muciniphila and Rikenellaceae and the decrease of other taxa like Lactobacillaceae. Using an in vitro gut model, we further showed that the probiotic mixture favours the production of butyrate and propionate. Our findings provide crucial clues for the design and use of more efficient probiotic preparations in obesity management and may bring new insights into the mechanisms by which host-microbe interactions govern such protective effects.


PLOS ONE | 2014

Local and systemic immune mechanisms underlying the anti-colitis effects of the dairy bacterium Lactobacillus delbrueckii.

Clarissa Santos Rocha; Ana Cristina Gomes-Santos; Thais Garcias Moreira; Marcela de Azevedo; Tessalia Diniz Luerce; Mahendra Mariadassou; Ana Paula Longaray Delamare; Philippe Langella; Emmanuelle Maguin; Vasco Azevedo; Ana Maria Caetano Faria; Anderson Miyoshi; Maarten van de Guchte

Several probiotic bacteria have been proposed for treatment or prevention of inflammatory bowel diseases (IBD), showing a protective effect in animal models of experimental colitis and for some of them also in human clinical trials. While most of these probiotic bacteria are isolated from the digestive tract, we recently reported that a Lactobacillus strain isolated from cheese, L. delbrueckii subsp. lactis CNRZ327 (Lb CNRZ327), also possesses anti-inflammatory effects in vitro and in vivo, demonstrating that common dairy bacteria may be useful in the treatment or prevention of IBD. Here, we studied the mechanisms underlying the protective effects of Lb CNRZ327 in vivo, in a mouse dextran sodium sulfate (DSS) colitis model. During colitis, Lb CNRZ327 modulated the production of TGF-β, IL-6, and IL-12 in colonic tissue and of TGF-β and IL-6 in the spleen, and caused an expansion of CD4+Foxp3+ regulatory T cells in the cecal lymph nodes. Moreover, a strong tendency to CD4+Foxp3+ expansion was also observed in the spleen. The results of this study for the first time show that orally administered dairy lactobacilli can not only modulate mucosal but also systemic immune responses and constitute an effective treatment of IBD.


Bioinformatics | 2018

FROGS: Find, Rapidly, OTUs with Galaxy Solution

Frédéric Escudié; Lucas Auer; Maria Bernard; Mahendra Mariadassou; Laurent Cauquil; Katia Vidal; Sarah Maman; Guillermina Hernandez-Raquet; Sylvie Combes; Géraldine Pascal

Motivation Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own. Results This Galaxy‐supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross‐sample validation. The taxonomic affiliation returns an innovative multi‐affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME. Availability and implementation Source code and instructions for installation: https://github.com/geraldinepascal/FROGS.git. A companion website: http://frogs.toulouse.inra.fr. Supplementary information Supplementary data are available at Bioinformatics online.


Metabolic Engineering | 2015

Quantitative prediction of genome-wide resource allocation in bacteria.

Anne Goelzer; Jan Muntel; Victor Chubukov; Matthieu Jules; Eric Prestel; Rolf Nölker; Mahendra Mariadassou; Stéphane Aymerich; Michael Hecker; Philippe Noirot; Dörte Becher; Vincent Fromion

Predicting resource allocation between cell processes is the primary step towards decoding the evolutionary constraints governing bacterial growth under various conditions. Quantitative prediction at genome-scale remains a computational challenge as current methods are limited by the tractability of the problem or by simplifying hypotheses. Here, we show that the constraint-based modeling method Resource Balance Analysis (RBA), calibrated using genome-wide absolute protein quantification data, accurately predicts resource allocation in the model bacterium Bacillus subtilis for a wide range of growth conditions. The regulation of most cellular processes is consistent with the objective of growth rate maximization except for a few suboptimal processes which likely integrate more complex objectives such as coping with stressful conditions and survival. As a proof of principle by using simulations, we illustrated how calibrated RBA could aid rational design of strains for maximizing protein production, offering new opportunities to investigate design principles in prokaryotes and to exploit them for biotechnological applications.


Ecology Letters | 2015

Microbial ecosystems are dominated by specialist taxa

Mahendra Mariadassou; Samuel Pichon; Dieter Ebert

Abundance and specificity are two key characteristics of species distribution and biodiversity. Theories of species assembly aim to reproduce the empirical joint patterns of specificity and abundance, with the goal to explain patterns of biodiversity across habitats. The specialist-generalist paradigm predicts that specialists should have a local advantage over generalists and thus be more abundant. We developed a specificity index to analyse abundance-specificity relationships in microbial ecosystems. By analysing microbiota spanning 23 habitats from three very different data sets covering a wide range of sequencing depths and environmental conditions, we find that habitats are consistently dominated by specialist taxa, resulting in a strong, positive correlation between abundance and specificity. This finding is consistent over several levels of taxonomic aggregation and robust to errors in abundance measures. The relationship explains why shallow sequencing captures similar β-diversity as deep sequencing, and can be sufficient to capture the habitat-specific functions of microbial communities.


PeerJ | 2016

Multiple comparative metagenomics using multiset k-mer counting

Gaëtan Benoit; Pierre Peterlongo; Mahendra Mariadassou; Erwan Drezen; Sophie Schbath; Dominique Lavenier; Claire Lemaitre

Background Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can be associated to known organisms. On the other hand, de novo methods, that compare the whole sets of sequences, either do not scale up on ambitious metagenomic projects or do not provide precise and exhaustive results. Methods These limitations motivated the development of a new de novo metagenomic comparative method, called Simka. This method computes a large collection of standard ecological distances by replacing species counts by k-mer counts. Simka scales-up today’s metagenomic projects thanks to a new parallel k-mer counting strategy on multiple datasets. Results Experiments on public Human Microbiome Project datasets demonstrate that Simka captures the essential underlying biological structure. Simka was able to compute in a few hours both qualitative and quantitative ecological distances on hundreds of metagenomic samples (690 samples, 32 billions of reads). We also demonstrate that analyzing metagenomes at the k-mer level is highly correlated with extremely precise de novo comparison techniques which rely on all-versus-all sequences alignment strategy or which are based on taxonomic profiling.


Evolution | 2016

The Red Queen lives: Epistasis between linked resistance loci.

César M. J. A. Metzger; Pepijn Luijckx; Gilberto Bento; Mahendra Mariadassou; Dieter Ebert

A popular theory explaining the maintenance of genetic recombination (sex) is the Red Queen Theory. This theory revolves around the idea that time‐lagged negative frequency‐dependent selection by parasites favors rare host genotypes generated through recombination. Although the Red Queen has been studied for decades, one of its key assumptions has remained unsupported. The signature host‐parasite specificity underlying the Red Queen, where infection depends on a match between host and parasite genotypes, relies on epistasis between linked resistance loci for which no empirical evidence exists. We performed 13 genetic crosses and tested over 7000 Daphnia magna genotypes for resistance to two strains of the bacterial pathogen Pasteuria ramosa. Results reveal the presence of strong epistasis between three closely linked resistance loci. One locus masks the expression of the other two, while these two interact to produce a single resistance phenotype. Changing a single allele on one of these interacting loci can reverse resistance against the tested parasites. Such a genetic mechanism is consistent with host and parasite specificity assumed by the Red Queen Theory. These results thus provide evidence for a fundamental assumption of this theory and provide a genetic basis for understanding the Red Queen dynamics in the Daphnia–Pasteuria system.


Bernoulli | 2015

Convergence of the groups posterior distribution in latent or stochastic block models

Mahendra Mariadassou; Catherine Matias

We propose a unified framework for studying both latent and stochastic block models, which are used to cluster simultaneously rows and columns of a data matrix. In this new framework, we study the behaviour of the groups posterior distribution, given the data. We characterize whether it is possible to asymptotically recover the actual groups on the rows and columns of the matrix. In other words, we establish sufficient conditions for the groups posterior distribution to converge (as the size of the data increases) to a Dirac mass located at the actual (random) groups configuration. In particular, we highlight some cases where the model assumes symmetries in the matrix of connection probabilities that prevents from a correct recovering of the groups. We also discuss the validity of these results when the proportion of non-null entries in the data matrix converges to zero.


Scientific Reports | 2017

Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study

Stéphanie-Marie Deutsch; Mahendra Mariadassou; Pierre Nicolas; Sandrine Parayre; Rozenn Le Guellec; Victoria Chuat; Vincent Péton; Caroline Le Maréchal; Julien Burati; Valentin Loux; Valérie Briard-Bion; Julien Jardin; Coline Plé; Benoît Foligné; Gwénaël Jan; Hélène Falentin

Propionibacterium freudenreichii, a dairy starter, can reach a population of almost 109 propionibacteria per gram in Swiss-type cheese at the time of consumption. Also consumed as a probiotic, it displays strain-dependent anti-inflammatory properties mediated by surface proteins that induce IL-10 in leukocytes. We selected 23 strains with varied anti-inflammatory potentials in order to identify the protein(s) involved. After comparative genomic analysis, 12 of these strains were further analysed by surface proteomics, eight of them being further submitted to transcriptomics. The omics data were then correlated to the anti-inflammatory potential evaluated by IL-10 induction. This comparative omics strategy highlighted candidate genes that were further subjected to gene-inactivation validation. This validation confirmed the contribution of surface proteins, including SlpB and SlpE, two proteins with SLH domains known to mediate non-covalent anchorage to the cell-wall. Interestingly, HsdM3, predicted as cytoplasmic and involved in DNA modification, was shown to contribute to anti-inflammatory activity. Finally, we demonstrated that a single protein cannot explain the anti-inflammatory properties of a strain. These properties therefore result from different combinations of surface and cytoplasmic proteins, depending on the strain. Our enhanced understanding of the molecular bases for immunomodulation will enable the relevant screening for bacterial resources with anti-inflammatory properties.


Evolution | 2015

High genetic variation in resting stage production in a metapopulation: Is there evidence for local adaptation?

Anne C. Roulin; Mahendra Mariadassou; Matthew D. Hall; Jean-Claude Walser; Christoph R. Haag; Dieter Ebert

Local adaptation is a key process for the maintenance of genetic diversity and population diversification. A better understanding of the mechanisms that allow (or prevent) local adaptation constitutes a key in apprehending how and at what spatial scale it occurs. The production of resting stages is found in many taxa and reflects an adaptation to outlast adverse environmental conditions. Daphnia magna (Crustacea) can alternate between asexual and sexual reproduction, the latter being linked to dormancy, as resting stages can only be produced sexually. In this species, on a continental scale, resting‐stage production is locally adapted—that is, it is induced when the photoperiod indicates the imminence of habitat deterioration. Here, we aimed to explore whether selection is strong enough to maintain local adaptation at a scale of a few kilometers. We assessed life‐history traits of 64 D. magna clones originating from 11 populations of a metapopulation with permanent and intermittent pool habitats. We found large within‐ and between‐population variation for all dormancy‐related traits, but no evidence for the hypothesized higher resting‐stage production in animals from intermittent habitats. We discuss how gene flow, founder events, or other forms of selection might interfere with the process of local adaptation.

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Valentin Loux

Institut national de la recherche agronomique

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Anne-Laure Abraham

Institut national de la recherche agronomique

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Hélène Falentin

Institut national de la recherche agronomique

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Lucas Auer

University of Toulouse

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Sophie Schbath

Institut national de la recherche agronomique

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Aurélie Nicolas

Institut national de la recherche agronomique

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Emmanuelle Maguin

Institut national de la recherche agronomique

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Gwénaël Jan

Institut national de la recherche agronomique

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