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2. Molecular Identification and Subtype Analysis of Blastocystis sp. Isolates from Wild Mussels (Mytilus edulis) in Northern France

Author

Ryckman, Manon, primary, Gantois, Nausicaa, additional, Dominguez, Ruben Garcia, additional, Desramaut, Jeremy, additional, Li, Luen-Luen, additional, Even, Gaël, additional, Audebert, Christophe, additional, Devos, Damien Paul, additional, Chabé, Magali, additional, Certad, Gabriela, additional, Monchy, Sébastien, additional, and Viscogliosi, Eric, additional

Published
2024
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3. Large-Scale Molecular Epidemiological Survey of Blastocystis sp. among Herbivores in Egypt and Assessment of Potential Zoonotic Risk.

Author

Naguib, Doaa, Gantois, Nausicaa, Desramaut, Jeremy, Dominguez, Ruben Garcia, Arafat, Nagah, Atwa, Samar Magdy, Even, Gaël, Devos, Damien Paul, Certad, Gabriela, Chabé, Magali, and Viscogliosi, Eric

Subjects
DIETARY patterns, MIXED infections, COLONIZATION (Ecology), MOLECULAR epidemiology, BLASTOCYSTIS, RUMINANTS
Abstract

Given the proven zoonotic potential of the intestinal protozoan Blastocystis sp., a fast-growing number of surveys are being conducted to identify potential animal reservoirs for transmission of the parasite. Nevertheless, few epidemiological studies have been conducted on farmed animals in Egypt. Therefore, a total of 1089 fecal samples were collected from herbivores (sheep, goats, camels, horses, and rabbits) in six Egyptian governorates (Dakahlia, Gharbia, Kafr El Sheikh, Giza, Aswan, and Sharqia). Samples were screened for the presence of Blastocystis sp. by real-time PCR followed by sequencing of positive PCR products and phylogenetic analysis for subtyping of the isolates. Overall, Blastocystis sp. was identified in 37.6% of the samples, with significant differences in frequency between animal groups (sheep, 65.5%; camels, 62.2%; goats, 36.0%; rabbits, 10.1%; horses, 3.3%). Mixed infections were reported in 35.7% of the Blastocystis sp.-positive samples. A wide range of subtypes (STs) with varying frequency were identified from single infections in ruminants including sheep (ST1–ST3, ST5, ST10, ST14, ST21, ST24, ST26, and ST40), goats (ST1, ST3, ST5, ST10, ST26, ST40, ST43, and ST44), and camels (ST3, ST10, ST21, ST24–ST26, ST30, and ST44). Most of them overlapped across these animal groups, highlighting their adaptation to ruminant hosts. In other herbivores, only three and two STs were evidenced in rabbits (ST1–ST3) and horses (ST3 and ST44), respectively. The greater occurrence and wider genetic diversity of parasite isolates among ruminants, in contrast to other herbivores, strongly suggested that dietary habits likely played a significant role in influencing both the colonization rates of Blastocystis sp. and ST preference. Of all the isolates subtyped herein, 66.3% were reported as potentially zoonotic, emphasizing the significant role these animal groups may play in transmitting the parasite to humans. These findings also expand our knowledge on the prevalence, genetic diversity, host specificity, and zoonotic potential of Blastocystis sp. in herbivores. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Molecular Epidemiology and Genetic Diversity of the Enteric Protozoan Parasite Blastocystis sp. in the Northern Egypt Population

Author

Naguib, Doaa, primary, Gantois, Nausicaa, additional, Desramaut, Jeremy, additional, Arafat, Nagah, additional, Mandour, Mohamed, additional, Abdelmaogood, Asmaa Kamal Kamal, additional, Mosa, Ashraf Fawzy, additional, Denoyelle, Constance, additional, Even, Gaël, additional, Certad, Gabriela, additional, Chabé, Magali, additional, and Viscogliosi, Eric, additional

Published
2023
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7. The effect of yeast-derived β-glucans in reducing the adverse outcome of Lawsonia intracellularis in finishing pigs.

Author

Rhayat, Lamya, Even, Gaël, Kiros, Tadele G., Kuhn, Géraldine, Lebrun-Ruer, Ségolène, Audebert, Christophe, and Schulthess, Julie

Subjects
BETA-glucans, ANIMAL herds, SWINE, MEMORY, DIETARY supplements
Abstract

Introduction: Chronic diarrhoea is one of the most recurrent health issues in pig herds. Among Q9 the causative agents of diarrhoea, Lawsonia intracellularis is quite frequent with worldwide distribution leading to detrimental economical losses, as a result of the poor growth rate of the infected pigs. A growing body of evidence has shown that branched yeast b-glucans are excellent inducers of innate immunity memory in humans and in pigs. Methods: In this study, yeast branched b-glucans were evaluated as a potential solution to control infection by L. intracellularis in pigs by reducing the shedding of L. intracellularis in the faeces of infected animals. To address this hypothesis, naturally infected grow finishing pigs were divided into two treatment groups (n = 80) and fed either with a basal diet (Control) or the same basal diet supplemented with 250 g/ton b-glucans (BG-fed group). Results: Our results have shown that BG-supplemented pigs during the growing and finishing period had significantly increased body weight (BW) by 4.22 kg on average on day 97 and ADG up to 5.6% over the whole experiment (p<5.0 x 10-2) with no significant increase in ADFI. Similarly, supplementation of pigs with BG during the grow-finish phase has significantly reduced (p<4.0x10-4) faecal shedding of the bacteria in infected pigs on day 97. Furthermore, our results indicate that microbial a-diversity was negatively correlated with the presence of L. intracellularis. Animals fed with yeast BG show a reduction of the two genera Sarcina and Catenibacterium and a deeper analysis indicated that the ratio of Fibrobacter to Lacnospiraceae_AC2044 group could be a potential marker for L. Intracellularis susceptibility. Conclusion: This study demonstrated the beneficial effect of adding branched yeast BG in the diet of grow-finish pigs in reducing the dissemination of L. intracellularis between pigs in a given herd. [ABSTRACT FROM AUTHOR]

Published
2023
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8. First Epidemiological Survey on the Prevalence and Subtypes Distribution of the Enteric Parasite Blastocystis sp. in Vietnam

Author

Nguyen, Linh Do Ngoc, primary, Gantois, Nausicaa, additional, Hoang, Trung Thanh, additional, Do, Bong Thi, additional, Desramaut, Jeremy, additional, Naguib, Doaa, additional, Tran, Tuan Ngoc, additional, Truong, Anh Duc, additional, Even, Gaël, additional, Certad, Gabriela, additional, Chabé, Magali, additional, and Viscogliosi, Eric, additional

Published
2023
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10. Putative SET-domain methyltransferases inCryptosporidium parvumand histone methylation during infection

Author

Sawant, Manasi, primary, Benamrouz-Vanneste, Sadia, additional, Meloni, Dionigia, additional, Gantois, Nausicaa, additional, Even, Gaël, additional, Guyot, Karine, additional, Creusy, Colette, additional, Duval, Erika, additional, Wintjens, René, additional, Weitzman, Jonathan B., additional, Chabe, Magali, additional, Viscogliosi, Eric, additional, and Certad, Gabriela, additional

Published
2022
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12. Putative SET-domain methyltransferases in Cryptosporidium parvum and histone methylation during infection.

Author

Sawant, Manasi, Benamrouz-Vanneste, Sadia, Meloni, Dionigia, Gantois, Nausicaa, Even, Gaël, Guyot, Karine, Creusy, Colette, Duval, Erika, Wintjens, René, Weitzman, Jonathan JB, Chabe, Magali, Viscogliosi, Eric, Certad, Gabriela, Sawant, Manasi, Benamrouz-Vanneste, Sadia, Meloni, Dionigia, Gantois, Nausicaa, Even, Gaël, Guyot, Karine, Creusy, Colette, Duval, Erika, Wintjens, René, Weitzman, Jonathan JB, Chabe, Magali, Viscogliosi, Eric, and Certad, Gabriela

Abstract

Cryptosporidium parvum is a leading cause of diarrhoeal illness worldwide being a significant threat to young children and immunocompromised patients, but the pathogenesis caused by this parasite remains poorly understood. C. parvum was recently linked with oncogenesis. Notably, the mechanisms of gene expression regulation are unexplored in Cryptosporidium and little is known about how the parasite impact host genome regulation. Here, we investigated potential histone lysine methylation, a dynamic epigenetic modification, during the life cycle of the parasite. We identified SET-domain containing proteins, putative lysine methyltransferases (KMTs), in the C. parvum genome and classified them phylogenetically into distinct subfamilies (namely CpSET1, CpSET2, CpSET8, CpKMTox and CpAKMT). Our structural analysis further characterized CpSET1, CpSET2 and CpSET8 as histone lysine methyltransferases (HKMTs). The expression of the CpSET genes varies considerably during the parasite life cycle and specific methyl-lysine antibodies showed dynamic changes in parasite histone methylation during development (CpSET1:H3K4; CpSET2:H3K36; CpSET8:H4K20). We investigated the impact of C. parvum infection on the host histone lysine methylation. Remarkably, parasite infection led to a considerable decrease in host H3K36me3 and H3K27me3 levels, highlighting the potential of the parasite to exploit the host epigenetic regulation to its advantage. This is the first study to describe epigenetic mechanisms occurring throughout the parasite life cycle and during the host-parasite interaction. A better understanding of histone methylation in both parasite and host genomes may highlight novel infection control strategies., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2022

13. Bact-to-Batch: A Microbiota-Based Tool to Determine Optimal Animal Allocation in Experimental Designs.

Author

Even, Gaël, Mouray, Anthony, Vandenabeele, Nicolas, Martel, Sophie, Merlin, Sophie, Lebrun-Ruer, Ségolène, Chabé, Magali, and Audebert, Christophe

Subjects
*LABORATORY animals, *EXPERIMENTAL design, *ANIMAL experimentation, *GUT microbiome, *ANIMAL housing, *MICE, *ANIMAL traps
Abstract

The basis of any animal experimentation begins with the housing of animals that should take into account the need for splitting animals into similar groups. Even if it is generally recommended to use the minimum number of animals necessary to obtain reliable and statistically significant results (3Rs rule), the allocation of animals is currently mostly based on randomness. Since variability in gut microbiota is an important confounding factor in animal experiments, the main objective of this study was to develop a new approach based on 16S rRNA gene sequencing analysis of the gut microbiota of animals participating in an experiment, in order to correctly assign the animals across batches. For this purpose, a pilot study was performed on 20 mouse faecal samples with the aim of establishing two groups of 10 mice as similar as possible in terms of their faecal microbiota fingerprinting assuming that this approach limits future analytical bias and ensures reproducibility. The suggested approach was challenged with previously published data from a third-party study. This new method allows to embrace the unavoidable microbiota variability between animals in order to limit artefacts and to provide an additional assurance for the reproducibility of animal experiments. [ABSTRACT FROM AUTHOR]

Published
2023
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15. Detection, Molecular Identification and Transmission of the Intestinal Protozoa Blastocystis sp. in Guinea from a Large-Scale Epidemiological Study Conducted in the Conakry Area

Author

Guilavogui, Timothé, primary, Gantois, Nausicaa, additional, Even, Gaël, additional, Desramaut, Jeremy, additional, Dautel, Ellena, additional, Denoyelle, Constance, additional, Cissé, Fode Ibrahima, additional, Touré, Salif Cherif, additional, Kourouma, Bakary Luther, additional, Sawant, Manasi, additional, Chabé, Magali, additional, Certad, Gabriela, additional, and Viscogliosi, Eric, additional

Published
2022
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18. Changes in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations

Author

Even, Gaël, Lokmer, Ana, Rodrigues, Jules, Audebert, Christophe, Viscogliosi, Eric, Segurel, Laure, Chabé, Magali, Gènes Diffusion [Douai], Plateforme d'expertises génomiques appliquées aux sciences expérimentales [Lille] (PEGASE-Biosciences), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the ANR (Agence Nationale de la Recherche) grant MICROREGAL (ANR-15-CE02-0003), as well as by a research price IDF-FRM (Institut Danone France—Fondation pour la Recherche Médicale) attributed to LS., ANR-15-CE02-0003,MICROREGAL,Adaptations du microbiome intestinal humain aux changements passés et présents d'alimentation et de mode de vies(2015), Réseau International des Instituts Pasteur (RIIP), Éco-Anthropologie (EAE), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Laure, Segurel, and Adaptations du microbiome intestinal humain aux changements passés et présents d'alimentation et de mode de vies - - MICROREGAL2015 - ANR-15-CE02-0003 - AAPG2015 - VALID

Subjects
Adult, Microbiology (medical), metagenomics, intestinal protozoa, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], gut microbiota, [SDV]Life Sciences [q-bio], Immunology, Microbiology, digestive system, Gastrointestinal Microbiome, Entamoeba, Feces, Cellular and Infection Microbiology, Infectious Diseases, RNA, Ribosomal, 16S, parasitic diseases, Blastocystis, [SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Humans, 16S rRNA gene, Cameroon, Original Research
Abstract

International audience; Human gut microbial communities are mainly composed of bacteria, but also include fungi, viruses, archaea, and protozoa, whose role in the gut ecosystem has only recently begun to be recognized. For example, humans colonized by Blastocystis (a gut protozoan with controversial pathogenicity) host a more diverse bacterial microbiota than individuals not carrying it, suggesting that its presence may be beneficial for the host. In parallel, the presence of non-pathogenic Entamoeba spp. has been associated with an increased diversity and compositional shifts in the bacterial microbiota of healthy rural individuals in Cameroon. However, Entamoeba and Blastocystis , the two most prevalent human gut protozoa, have never been studied in the same individuals, preventing the study of their interaction. As Blastocystis is one of the few gut protozoa commonly found in industrialized populations, which are otherwise mostly devoid of gut eukaryotes, we need to focus on rural “traditional” populations, who harbor a higher diversity of gut eukaryotes (whether pathogenic or commensal) in order to study protozoa interactions in the gut ecosystem. To this end, we profiled the gut bacterial microbiota of 134 healthy Cameroonian adults using 16S rRNA gene amplicon sequencing data. Entamoeba and Blastocystis presence and co-occurrence pattern in the same individuals were determined using metagenomic shotgun data. We found that, when taking into account both protozoa jointly, Blastocystis was associated with both a higher richness and a higher evenness of the gut bacterial microbiota, while Entamoeba was associated only with a higher richness. We demonstrated a cumulative influence of these protozoa on bacterial microbiome diversity. Furthermore, while the abundance of several common taxa (for example, Ruminococcaceae , Coprococcus and Butyrivibrio ) varied according to Blastocystis colonization, only a single Bacteroides amplicon sequence variant was found to be differentially abundant between Entamoeba -negative and Entamoeba -positive samples. Given the specific signature of each protozoan on the gut microbiota and the seemingly stronger association for Blastocystis , our results suggest that Blastocystis and Entamoeba interact with gut bacteria each in its own way, but experimental studies are needed to explore the precise mechanisms of these interactions.

Published
2021

19. Putative SET-domain methyltransferases in Cryptosporidium parvumand histone methylation during infection

Author

Sawant, Manasi, Benamrouz-Vanneste, Sadia, Meloni, Dionigia, Gantois, Nausicaa, Even, Gaël, Guyot, Karine, Creusy, Colette, Duval, Erika, Wintjens, René, Weitzman, Jonathan B., Chabe, Magali, Viscogliosi, Eric, and Certad, Gabriela

Abstract

ABSTRACTCryptosporidium parvumis a leading cause of diarrhoeal illness worldwide being a significant threat to young children and immunocompromised patients, but the pathogenesis caused by this parasite remains poorly understood. C. parvumwas recently linked with oncogenesis. Notably, the mechanisms of gene expression regulation are unexplored in Cryptosporidiumand little is known about how the parasite impact host genome regulation. Here, we investigated potential histone lysine methylation, a dynamic epigenetic modification, during the life cycle of the parasite. We identified SET-domain containing proteins, putative lysine methyltransferases (KMTs), in the C. parvumgenome and classified them phylogenetically into distinct subfamilies (namely CpSET1, CpSET2, CpSET8, CpKMTox and CpAKMT). Our structural analysis further characterized CpSET1, CpSET2 and CpSET8 as histone lysine methyltransferases (HKMTs). The expression of the CpSET genes varies considerably during the parasite life cycle and specific methyl-lysine antibodies showed dynamic changes in parasite histone methylation during development (CpSET1:H3K4; CpSET2:H3K36; CpSET8:H4K20). We investigated the impact of C. parvuminfection on the host histone lysine methylation. Remarkably, parasite infection led to a considerable decrease in host H3K36me3 and H3K27me3 levels, highlighting the potential of the parasite to exploit the host epigenetic regulation to its advantage. This is the first study to describe epigenetic mechanisms occurring throughout the parasite life cycle and during the host–parasite interaction. A better understanding of histone methylation in both parasite and host genomes may highlight novel infection control strategies.

Published
2022
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20. Blastocystis sp. Prevalence and Subtypes Distribution amongst Syrian Refugee Communities Living in North Lebanon

Author

Khaled, Salma, primary, Gantois, Nausicaa, additional, Ayoubi, Aisha, additional, Even, Gaël, additional, Sawant, Manasi, additional, El Houmayraa, Jinane, additional, Nabot, Mathieu, additional, Benamrouz-Vanneste, Sadia, additional, Chabé, Magali, additional, Certad, Gabriela, additional, El Safadi, Dima, additional, Dabboussi, Fouad, additional, Hamze, Monzer, additional, and Viscogliosi, Eric, additional

Published
2021
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21. Prevalence and Subtype Distribution of Blastocystis sp. in Senegalese School Children

Author

Khaled, Salma, primary, Gantois, Nausicaa, additional, Ly, Amadou Tidjani, additional, Senghor, Simon, additional, Even, Gaël, additional, Dautel, Ellena, additional, Dejager, Romane, additional, Sawant, Manasi, additional, Baydoun, Martha, additional, Benamrouz-Vanneste, Sadia, additional, Chabé, Magali, additional, Ndiaye, Seynabou, additional, Schacht, Anne-Marie, additional, Certad, Gabriela, additional, Riveau, Gilles, additional, and Viscogliosi, Eric, additional

Published
2020
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22. Prevalence, Molecular Identification, and Risk Factors for Cryptosporidium Infection in Edible Marine Fish: A Survey Across Sea Areas Surrounding France

Author

Certad, Gabriela, Follet, Jérôme, Gantois, Nausicaa, Hammouma-ghelboun, Ourida, Guyot, Karine, Benamrouz-vanneste, Sadia, Fréalle, Emilie, Seesao, Yuwalee, Delaire, Baptiste, Creusy, Colette, Even, Gaël, Verrez-bagnis, Veronique, Ryan, Una, Gay, Mélanie, Aliouat-denis, Cécile, Viscogliosi, Eric, Certad, Gabriela, Follet, Jérôme, Gantois, Nausicaa, Hammouma-ghelboun, Ourida, Guyot, Karine, Benamrouz-vanneste, Sadia, Fréalle, Emilie, Seesao, Yuwalee, Delaire, Baptiste, Creusy, Colette, Even, Gaël, Verrez-bagnis, Veronique, Ryan, Una, Gay, Mélanie, Aliouat-denis, Cécile, and Viscogliosi, Eric

Abstract

Cryptosporidium, a zoonotic pathogen, is able to infect a wide range of hosts including wild and domestic animals, and humans. Although it is well known that some parasites are both fish pathogens and recognized agents of zoonosis with a public health impact, little information is available concerning the prevalence of Cryptosporidium in wild aquatic environments. To evaluate the prevalence of Cryptosporidium spp. in commercially important edible marine fish in different European seas (English channel, North sea, Bay of Biscay, Celtic sea and Mediterranean sea), 1,853 specimens were collected as part of two surveys. Nested PCR followed by sequence analysis at the 18S rRNA gene locus was used to identify Cryptosporidium spp. The overall prevalence of Cryptosporidium spp. in sampled fish reached 2.3% (35 out of 1,508) in a first campaign and 3.2% (11 out of 345) in a second campaign. Sequence and phylogenetic analysis of positive samples identified Cryptosporidium parvum (n = 10) and seven genotypes which exhibited between 7.3 and 10.1% genetic distance from C. molnari, with the exception of one genotype which exhibited only 0.5–0.7% genetic distance from C. molnari. Among 31 analyzed fish species, 11 (35.5%) were identified as potential hosts for Cryptosporidium. A higher prevalence of Cryptosporidium spp. was observed in larger fish, in fish collected during the spring-summer period, and in those caught in the North East Atlantic. Pollachius virens (saithe) was the most frequently Cryptosporidium positive species. In fish infected by other parasites, the risk of being Cryptosporidium positive increased 10-fold (OR: 9.95, CI: 2.32–40.01.04, P = 0.0002). Four gp60 subtypes were detected among the C. parvum positive samples: IIaA13G1R1, IIaA15G2R1, IIaA17G2R1, and IIaA18G3R1. These C. parvum subtypes have been previously detected in terrestrial mammals and may constitute an additional source of infection for other animals and in particular for humans. Microscopical exa

Published
2019
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26. Prevalence, Molecular Identification, and Risk Factors for Cryptosporidium Infection in Edible Marine Fish: A Survey Across Sea Areas Surrounding France

Author

Certad, Gabriela, primary, Follet, Jérôme, additional, Gantois, Nausicaa, additional, Hammouma-Ghelboun, Ourida, additional, Guyot, Karine, additional, Benamrouz-Vanneste, Sadia, additional, Fréalle, Emilie, additional, Seesao, Yuwalee, additional, Delaire, Baptiste, additional, Creusy, Colette, additional, Even, Gaël, additional, Verrez-Bagnis, Véronique, additional, Ryan, Una, additional, Gay, Mélanie, additional, Aliouat-Denis, Cécile, additional, and Viscogliosi, Eric, additional

Published
2019
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27. The Formation of Glycan-Specific Natural Antibodies Repertoire in GalT-KO Mice Is Determined by Gut Microbiota

Author

Bello-Gil, Daniel, primary, Audebert, Christophe, additional, Olivera-Ardid, Sara, additional, Pérez-Cruz, Magdiel, additional, Even, Gaël, additional, Khasbiullina, Nailya, additional, Gantois, Nausicaa, additional, Shilova, Nadezhda, additional, Merlin, Sophie, additional, Costa, Cristina, additional, Bovin, Nicolai, additional, and Mañez, Rafael, additional

Published
2019
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30. Use of a novel evolutionary algorithm for genomic selection

Author

Hamon, Julie, Even, Gaël, Dassonneville, Romain, Jacques, Julien, Dhaenens, Clarisse, Parallel Cooperative Multi-criteria Optimization (DOLPHIN), Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Gènes Diffusion [Douai], Plateforme d'expertises génomiques appliquées aux sciences expérimentales [Lille] (PEGASE-Biosciences), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), MOdel for Data Analysis and Learning (MODAL), Laboratoire Paul Painlevé - UMR 8524 (LPP), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-École polytechnique universitaire de Lille (Polytech Lille), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, UF Génopathies, Laboratoire de Biochimie et Biologie Moléculaire, Université de Lille, Sciences et Technologies-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Hamon, Julie, Laboratoire Paul Painlevé (LPP), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Université de Lille-Centre National de la Recherche Scientifique (CNRS), and UF Génopathies - Laboratoire de Biochimie et Biologie Moléculaire [Lille] (LBBM)

Subjects
[MATH.MATH-CO] Mathematics [math]/Combinatorics [math.CO], [INFO.INFO-BT] Computer Science [cs]/Biotechnology, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], [MATH.MATH-CO]Mathematics [math]/Combinatorics [math.CO], combinatorial optimization, regression, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], genomic selection
Abstract

Background: In the context of genomic selection in animal breeding, animportant objective is to look for explicative markers for a phenotype understudy. The challenge of this study was to propose a model, based on a smallnumber of markers, to predict a quantitative trait. To deal with a high number ofmarkers, we propose using combinatorial optimization to perform variableselection, associated with a multiple regression model in a first approach and amixed model in a second, to predict the phenotype.Results:The efficiency of our two approaches, the first assuming that animals areindependent and the second integrating familial relationships, was evaluated onreal datasets. This reveals the importance of taking familial relationships intoaccount as the performances of the second approach were better. For example,on PIC data the correlation is around 0.15 higher using our approach takingfamilial relationships into account than with the Lasso bounded to 96 selectedmarkers. We also studied the importance of familial relationships on phenotypeswith different heritabilities. Finally, we compared our approaches with classicapproaches and obtained comparable results, sometimes better.Conclusion: This study shows the relevance of combining combinatorialoptimization with a regression model to propose a predictive model based on areasonable number of markers. Although this implies more parameters to beestimated and, therefore, takes longer to execute, it seems interesting to use amixed model in order to take familial relationships between animals into account.

Published
2015

32. Modèles mixtes en génétique animale : sélection de variables par optimisation combinatoire

Author

Hamon, Julie, Dhaenens, Clarisse, Even, Gaël, Jacques, Julien, Parallel Cooperative Multi-criteria Optimization (DOLPHIN), Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS), Gènes Diffusion [Douai], MOdel for Data Analysis and Learning (MODAL), Laboratoire Paul Painlevé - UMR 8524 (LPP), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-École polytechnique universitaire de Lille (Polytech Lille), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Hamon, Julie, Laboratoire Paul Painlevé (LPP), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, and Université de Lille-Centre National de la Recherche Scientifique (CNRS)

Subjects
[STAT.AP]Statistics [stat]/Applications [stat.AP], [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [STAT.AP] Statistics [stat]/Applications [stat.AP], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

National audience; En sélection génomique animale, un des enjeux consiste à identifier un sous-ensemble de marqueurs génomiques explicatifs pour un trait d'intérêt quantitatif. La spécificité des études animales nécessite l'utilisation de modèles mixtes, du fait des liens de parenté entre individus. Nous proposons d'effectuer, dans ce cadre, une sélection des marqueurs d'intérêt à l'aide de méthodes d'optimisation combinatoire.

Published
2013

33. Coopération entre Optimisation Combinatoire et Statistiques pour la Sélection animale

Author

Hamon, Julie, Dhaenens, Clarisse, Jacques, Julien, Even, Gaël, Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS), Parallel Cooperative Multi-criteria Optimization (DOLPHIN), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria), Laboratoire Paul Painlevé (LPP), Université de Lille-Centre National de la Recherche Scientifique (CNRS), MOdel for Data Analysis and Learning (MODAL), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-École polytechnique universitaire de Lille (Polytech Lille), Gènes Diffusion [Douai], Laboratoire Paul Painlevé - UMR 8524 (LPP), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Hamon, Julie, and Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]

Subjects
[INFO.INFO-RO] Computer Science [cs]/Operations Research [cs.RO], [STAT.TH] Statistics [stat]/Statistics Theory [stat.TH], [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], [STAT.TH]Statistics [stat]/Statistics Theory [stat.TH], [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST]
Abstract

National audience; L'objectif de cette étude est d'élaborer des modèles prédictifs permettant, à partir de données génomiques, de déterminer les individus les plus performants selon certains critères quantitatifs. L'approche proposée allie les forces des méthodes statistiques et des méthodes d'optimisation combinatoire.

Published
2012

34. Combining combinatorial optimization and statistics to mine high-throughput genotyping data

Author

Hamon, Julie, Dhaenens, Clarisse, Jacques, Julien, Even, Gaël, Parallel Cooperative Multi-criteria Optimization (DOLPHIN), Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS), Laboratoire Paul Painlevé (LPP), Université de Lille-Centre National de la Recherche Scientifique (CNRS), MOdel for Data Analysis and Learning (MODAL), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-École polytechnique universitaire de Lille (Polytech Lille), Gènes Diffusion [Douai], Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL], Hamon, Julie, Laboratoire Paul Painlevé - UMR 8524 (LPP), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, and Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe

Subjects
Genomic selection, Optimization, Regression, [INFO.INFO-RO] Computer Science [cs]/Operations Research [cs.RO], [STAT.TH] Statistics [stat]/Statistics Theory [stat.TH], [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], regression, [STAT.TH]Statistics [stat]/Statistics Theory [stat.TH], [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST], optimization, genomic selection
Abstract

National audience; Depuis quelques années, la génomique a grandement évolué avec le développement de nouvelles technologies telles que le séquençage et le génotypage haut-débit. En ce qui concerne le domaine animal, nous sommes aujourd'hui capables de lire les informations génomiques sur près de 800 000 marqueurs sur des ensembles d'individus de plus en plus larges (de 3 000 à 10 000). Ces données peuvent donner lieu à des études d'association entre les marqueurs (GWAS : Genome-Wide Association Studies). Outre les contraintes biologiques (stockage des échantillons, manipulations longues et coûteuses...), la partie analyse de données (étude et extraction de connaissances) doit aussi être adaptée en terme de méthodologie et d'architecture matérielle et logicielle. L'objectif est d'élaborer des modéles prédictifs permettant, à partir des données génomiques, de déterminer les individus les plus performants selon certains critères quantitatifs de sélection animale. Pour cela, l'objectif théorique est à terme de définir de nouvelles méthodes permettant la coopération entre statistique et optimisation combinatoire spécifiquement dédiées aux données issues de génotypage haut débit en vue d'une implémentation.

Published
2011

38. Putative SET-domain methyltransferases in Cryptosporidium parvum and histone methylation during infection.

Author

Sawant M, Benamrouz-Vanneste S, Meloni D, Gantois N, Even G, Guyot K, Creusy C, Duval E, Wintjens R, Weitzman JB, Chabe M, Viscogliosi E, and Certad G

Subjects
Child, Preschool, Epigenesis, Genetic, Histone-Lysine N-Methyltransferase genetics, Histone-Lysine N-Methyltransferase metabolism, Histones genetics, Humans, Lysine genetics, Lysine metabolism, Methylation, Cryptosporidiosis, Cryptosporidium, Cryptosporidium parvum genetics, Cryptosporidium parvum metabolism
Abstract

Cryptosporidium parvum is a leading cause of diarrhoeal illness worldwide being a significant threat to young children and immunocompromised patients, but the pathogenesis caused by this parasite remains poorly understood. C. parvum was recently linked with oncogenesis. Notably, the mechanisms of gene expression regulation are unexplored in Cryptosporidium and little is known about how the parasite impact host genome regulation. Here, we investigated potential histone lysine methylation, a dynamic epigenetic modification, during the life cycle of the parasite. We identified SET-domain containing proteins, putative lysine methyltransferases (KMTs), in the C. parvum genome and classified them phylogenetically into distinct subfamilies (namely CpSET1, CpSET2, CpSET8, CpKMTox and CpAKMT). Our structural analysis further characterized CpSET1, CpSET2 and CpSET8 as histone lysine methyltransferases (HKMTs). The expression of the CpSET genes varies considerably during the parasite life cycle and specific methyl-lysine antibodies showed dynamic changes in parasite histone methylation during development (CpSET1:H3K4; CpSET2:H3K36; CpSET8:H4K20). We investigated the impact of C. parvum infection on the host histone lysine methylation. Remarkably, parasite infection led to a considerable decrease in host H3K36me3 and H3K27me3 levels, highlighting the potential of the parasite to exploit the host epigenetic regulation to its advantage. This is the first study to describe epigenetic mechanisms occurring throughout the parasite life cycle and during the host-parasite interaction. A better understanding of histone methylation in both parasite and host genomes may highlight novel infection control strategies.

Published
2022
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39. Changes in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations.

Author

Even G, Lokmer A, Rodrigues J, Audebert C, Viscogliosi E, Ségurel L, and Chabé M

Subjects
Adult, Feces, Humans, RNA, Ribosomal, 16S genetics, Blastocystis genetics, Entamoeba genetics, Gastrointestinal Microbiome
Abstract

Human gut microbial communities are mainly composed of bacteria, but also include fungi, viruses, archaea, and protozoa, whose role in the gut ecosystem has only recently begun to be recognized. For example, humans colonized by Blastocystis (a gut protozoan with controversial pathogenicity) host a more diverse bacterial microbiota than individuals not carrying it, suggesting that its presence may be beneficial for the host. In parallel, the presence of non-pathogenic Entamoeba spp. has been associated with an increased diversity and compositional shifts in the bacterial microbiota of healthy rural individuals in Cameroon. However, Entamoeba and Blastocystis , the two most prevalent human gut protozoa, have never been studied in the same individuals, preventing the study of their interaction. As Blastocystis is one of the few gut protozoa commonly found in industrialized populations, which are otherwise mostly devoid of gut eukaryotes, we need to focus on rural "traditional" populations, who harbor a higher diversity of gut eukaryotes (whether pathogenic or commensal) in order to study protozoa interactions in the gut ecosystem. To this end, we profiled the gut bacterial microbiota of 134 healthy Cameroonian adults using 16S rRNA gene amplicon sequencing data. Entamoeba and Blastocystis presence and co-occurrence pattern in the same individuals were determined using metagenomic shotgun data. We found that, when taking into account both protozoa jointly, Blastocystis was associated with both a higher richness and a higher evenness of the gut bacterial microbiota, while Entamoeba was associated only with a higher richness. We demonstrated a cumulative influence of these protozoa on bacterial microbiome diversity. Furthermore, while the abundance of several common taxa (for example, Ruminococcaceae , Coprococcus and Butyrivibrio ) varied according to Blastocystis colonization, only a single Bacteroides amplicon sequence variant was found to be differentially abundant between Entamoeba -negative and Entamoeba -positive samples. Given the specific signature of each protozoan on the gut microbiota and the seemingly stronger association for Blastocystis , our results suggest that Blastocystis and Entamoeba interact with gut bacteria each in its own way, but experimental studies are needed to explore the precise mechanisms of these interactions., Competing Interests: GE and CA are employed by the company Gènes Diffusion. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Even, Lokmer, Rodrigues, Audebert, Viscogliosi, Ségurel and Chabé.)

Published
2021
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