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1. The transplantation of the gut microbiome of fat-1 mice protects against colonic mucus layer disruption and endoplasmic reticulum stress induced by high fat diet

Author: Amina Bourragat, Quentin Escoula, Sandrine Bellenger, Olivier Zemb, Martin Beaumont, Killian Chaumonnot, Jean-Pierre Farine, Emmanuel Jacotot, Aline Bonnotte, Laure Avoscan, Jeanine Lherminier, Kangjia Luo, Michel Narce, and Jérôme Bellenger
Subjects: Obesity, mucus layer- ER stress, gut permeability, omega-3 polyunsaturated fatty acids, microbiome transplantation, Diseases of the digestive system. Gastroenterology, RC799-869
Abstract: ABSTRACTHigh-fat diets alter gut barrier integrity, leading to endotoxemia by impacting epithelial functions and inducing endoplasmic reticulum (ER) stress in intestinal secretory goblet cells. Indeed, ER stress, which is an important contributor to many chronic diseases such as obesity and obesity-related disorders, leads to altered synthesis and secretion of mucins that form the protective mucus barrier. In the present study, we investigated the relative contribution of omega-3 polyunsaturated fatty acid (PUFAs)-modified microbiota to alleviating alterations in intestinal mucus layer thickness and preserving gut barrier integrity. Male fat-1 transgenic mice (exhibiting endogenous omega-3 PUFAs tissue enrichment) and wild-type (WT) littermates were fed either an obesogenic high-fat diet (HFD) or a control diet. Unlike WT mice, HFD-fed fat-1 mice were protected against mucus layer alterations as well as an ER stress-mediated decrease in mucin expression. Moreover, cecal microbiota transferred from fat-1 to WT mice prevented changes in the colonic mucus layer mainly through colonic ER stress downregulation. These findings highlight a novel feature of the preventive effects of omega-3 fatty acids against intestinal permeability in obesity-related conditions.
Published: 2024
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2. The potential of microbiota information to better predict efficiency traits in growing pigs fed a conventional and a high-fiber diet

Author: Vanille Déru, Francesco Tiezzi, Céline Carillier-Jacquin, Benoit Blanchet, Laurent Cauquil, Olivier Zemb, Alban Bouquet, Christian Maltecca, and Hélène Gilbert
Subjects: Animal culture, SF1-1100, Genetics, QH426-470
Abstract: Abstract Background Improving pigs’ ability to digest diets with an increased dietary fiber content is a lever to improve feed efficiency and limit feed costs in pig production. The aim of this study was to determine whether information on the gut microbiota and host genetics can contribute to predict digestive efficiency (DE, i.e. digestibility coefficients of energy, organic matter, and nitrogen), feed efficiency (FE, i.e. feed conversion ratio and residual feed intake), average daily gain, and daily feed intake phenotypes. Data were available for 1082 pigs fed a conventional or high-fiber diet. Fecal samples were collected at 16 weeks, and DE was estimated using near‑infrared spectrometry. A cross-validation approach was used to predict traits within the same diet, for the opposite diet, and for a combination of both diets, by implementing three models, i.e. with only genomic (Gen), only microbiota (Micro), and both genomic and microbiota information (Micro+Gen). The predictive ability with and without sharing common sires and breeding environment was also evaluated. Prediction accuracy of the phenotypes was calculated as the correlation between model prediction and phenotype adjusted for fixed effects. Results Prediction accuracies of the three models were low to moderate ( 0.52). Prediction accuracies were not affected by the stratification of diets in the reference and validation sets and were in the same order of magnitude within the same diet, for the opposite diet, and for the combination of both diets. Prediction accuracies of the three models were significantly higher when pigs in the reference and validation populations shared common sires and breeding environment than when they did not (P
Published: 2024
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3. Genome wide association study of growth and feed efficiency traits in rabbits

Author: Hervé Garreau, Yann Labrune, Hervé Chapuis, Julien Ruesche, Juliette Riquet, Julie Demars, Florence Benitez, François Richard, Laurence Drouilhet, Olivier Zemb, and Hélène Gilbert
Subjects: feed efficiency, snp, gwas, genetics, candidate genes, rabbits, Animal culture, SF1-1100, Veterinary medicine, SF600-1100
Abstract: Feed efficiency is a major production trait in animal genetic breeding schemes. To further investigate the genetic control of feed efficiency in rabbits, we performed a genome-wide association study (GWAS) for growth and feed efficiency on 679 rabbits genotyped with the Affimetrix Axiom Rabbit 200K Genotyping Array. After quality control, 127 847 single-nucleotide polymorphisms (SNP) were retained for association analyses. The GWAS were performed using GEMMA software, applying a mixed univariate animal model with a linear regression on each SNP allele. The traits analysed were weight at weaning and at 63 days of age, average daily gain, total individual feed intake, feed conversion ratio and residual feed intake. No significant SNP was found for growth traits or feed intake. Fifteen genome-wide significant SNPs were detected for feed conversion ratio on OCU7, spanning from 124.8 Mbp to 126.3 Mbp, plus two isolated SNP on OCU2 (77.3 Mbp) and OCU8 (16.5 Mbp). For residual feed intake, a region on OCU18 (46.1-53.0 Mbp) was detected, which contained a putative functional candidate gene, GOT1.
Published: 2023
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4. Gut microbiota and host genetics contribute to the phenotypic variation of digestive and feed efficiency traits in growing pigs fed a conventional and a high fiber diet

Author: Vanille Déru, Francesco Tiezzi, Céline Carillier-Jacquin, Benoit Blanchet, Laurent Cauquil, Olivier Zemb, Alban Bouquet, Christian Maltecca, and Hélène Gilbert
Subjects: Animal culture, SF1-1100, Genetics, QH426-470
Abstract: Abstract Background Breeding pigs that can efficiently digest alternative diets with increased fiber content is a viable strategy to mitigate the feed cost in pig production. This study aimed at determining the contribution of the gut microbiota and host genetics to the phenotypic variability of digestive efficiency (DE) traits, such as digestibility coefficients of energy, organic matter and nitrogen, feed efficiency (FE) traits (feed conversion ratio and residual feed intake) and growth traits (average daily gain and daily feed intake). Data were available for 791 pigs fed a conventional diet and 735 of their full-sibs fed a high-fiber diet. Fecal samples were collected at 16 weeks of age to sequence the V3–V4 regions of the 16S ribosomal RNA gene and predict DE with near-infrared spectrometry. The proportions of phenotypic variance explained by the microbiota (microbiability) were estimated under three OTU filtering scenarios. Then, microbiability and heritability were estimated independently (models Micro and Gen) and jointly (model Micro+Gen) using a Bayesian approach for all traits. Breeding values were estimated in models Gen and Micro+Gen. Results Differences in microbiability estimates were significant between the two extreme filtering scenarios (14,366 and 803 OTU) within diets, but only for all DE. With the intermediate filtering scenario (2399 OTU) and for DE, microbiability was higher (> 0.44) than heritability (
Published: 2022
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5. Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs

Author: Amir Aliakbari, Olivier Zemb, Laurent Cauquil, Céline Barilly, Yvon Billon, and Hélène Gilbert
Subjects: Animal culture, SF1-1100, Genetics, QH426-470
Abstract: Abstract Background The objective of the present study was to investigate how variation in the faecal microbial composition is associated with variation in average daily gain (ADG), backfat thickness (BFT), daily feed intake (DFI), feed conversion ratio (FCR), and residual feed intake (RFI), using data from two experimental pig lines that were divergent for feed efficiency. Estimates of microbiability were obtained by a Bayesian approach using animal mixed models. Microbiome-wide association analyses (MWAS) were conducted by single-operational taxonomic units (OTU) regression and by back-solving solutions of best linear unbiased prediction using a microbiome covariance matrix. In addition, accuracy of microbiome predictions of phenotypes using the microbiome covariance matrix was evaluated. Results Estimates of heritability ranged from 0.31 ± 0.13 for FCR to 0.51 ± 0.10 for BFT. Estimates of microbiability were lower than those of heritability for all traits and were 0.11 ± 0.09 for RFI, 0.20 ± 0.11 for FCR, 0.04 ± 0.03 for DFI, 0.03 ± 0.03 for ADG, and 0.02 ± 0.03 for BFT. Bivariate analyses showed a high microbial correlation of 0.70 ± 0.34 between RFI and FCR. The two approaches used for MWAS showed similar results. Overall, eight OTU with significant or suggestive effects on the five traits were identified. They belonged to the genera and families that are mainly involved in producing short-chain fatty acids and digestive enzymes. Prediction accuracy of phenotypes using a full model including the genetic and microbiota components ranged from 0.60 ± 0.19 to 0.78 ± 0.05. Similar accuracies of predictions of the microbial component were observed using models that did or did not include an additive animal effect, suggesting no interaction with the genetic effect. Conclusions Our results showed substantial associations of the faecal microbiome with feed efficiency related traits but negligible effects with growth traits. Microbiome data incorporated as a covariance matrix can be used to predict phenotypes of animals that do not (yet) have phenotypic information. Connecting breeding environment between training sets and predicted populations could be necessary to obtain reliable microbiome predictions.
Published: 2022
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6. Chronic dietary exposure to a glyphosate-based herbicide results in total or partial reversibility of plasma oxidative stress, cecal microbiota abundance and short-chain fatty acid composition in broiler hens

Author: Mathias Fréville, Anthony Estienne, Christelle Ramé, Gaëlle Lefort, Marine Chahnamian, Christophe Staub, Eric Venturi, Julie Lemarchand, Elise Maximin, Alice Hondelatte, Olivier Zemb, Cécile Canlet, Rodrigo Guabiraba, Pascal Froment, and Joëlle Dupont
Subjects: birds, glyphosate, metabolism, cecal microbiome, oxidative stress, Physiology, QP1-981
Abstract: Glyphosate-based herbicides (GBHs) are massively used in agriculture. However, few studies have investigated the effects of glyphosate-based herbicides on avian species although they are largely exposed via their food. Here, we investigated the potential reversibility of the effects of chronic dietary exposure to glyphosate-based herbicides in broiler hens. For 42 days, we exposed 32-week-old hens to glyphosate-based herbicides via their food (47 mg/kg/day glyphosate equivalent, glyphosate-based herbicides, n = 75) corresponding to half glyphosate’s no-observed-adverse-effect-level in birds. We compared their performance to that of 75 control animals (CT). Both groups (glyphosate-based herbicides and control animals) were then fed for 28 additional days without glyphosate-based herbicides exposure (Ex-glyphosate-based herbicides and Ex-control animals). Glyphosate-based herbicides temporarily increased the plasma glyphosate and AMPA (aminomethylphosphonic acid) concentrations. Glyphosate and aminomethylphosphonic acid mostly accumulated in the liver and to a lesser extent in the leg muscle and abdominal adipose tissue. Glyphosate-based herbicides also temporarily increased the gizzard weight and plasma oxidative stress monitored by TBARS (thiobarbituric acid reactive substances). Glyphosate-based herbicides temporarily decreased the cecal concentrations of propionate, isobutyrate and propionate but acetate and valerate were durably reduced. The cecal microbiome was also durably affected since glyphosate-based herbicides inhibited Barnesiella and favored Alloprevotella. Body weight, fattening, food intake and feeding behavior as well as plasma lipid and uric acid were unaffected by glyphosate-based herbicides. Taken together, our results show possible disturbances of the cecal microbiota associated with plasma oxidative stress and accumulation of glyphosate in metabolic tissues in response to dietary glyphosate-based herbicides exposure in broiler hens. Luckily, glyphosate-based herbicides at this concentration does not hamper growth and most of the effects on the phenotypes are reversible.
Published: 2022
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7. Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to-weaning transition

Author: Martin Beaumont, Charlotte Paës, Eloïse Mussard, Christelle Knudsen, Laurent Cauquil, Patrick Aymard, Céline Barilly, Béatrice Gabinaud, Olivier Zemb, Sandra Fourre, Roselyne Gautier, Corinne Lencina, Hélène Eutamène, Vassilia Theodorou, Cécile Canlet, and Sylvie Combes
Subjects: early life, intestinal barrier development, organoids, epithelium, maternal milk, solid food, metabolome, Diseases of the digestive system. Gastroenterology, RC799-869
Abstract: In suckling mammals, the onset of solid food ingestion is coincident with the maturation of the gut barrier. This ontogenic process is driven by the colonization of the intestine by the microbiota. However, the mechanisms underlying the microbial regulation of the intestinal development in early life are not fully understood. Here, we studied the co-maturation of the microbiota (composition and metabolic activity) and of the gut barrier at the suckling-to-weaning transition by using a combination of experiments in vivo (suckling rabbit model), ex vivo (Ussing chambers) and in vitro (epithelial cell lines and organoids). The microbiota composition, its metabolic activity, para-cellular epithelial permeability and the gene expression of key components of the gut barrier shifted sharply at the onset of solid food ingestion in vivo, despite milk was still predominant in the diet at that time. We found that cecal content sterile supernatant (i.e. containing a mixture of metabolites) obtained after the onset of solid food ingestion accelerated the formation of the epithelial barrier in Caco-2 cells in vitro and our results suggested that these effects were driven by the bacterial metabolite butyrate. Moreover, the treatment of organoids with cecal content sterile supernatant partially replicated in vitro the effects of solid food ingestion on the epithelial barrier in vivo. Altogether, our results show that the metabolites produced by the microbiota at the onset of solid food ingestion contribute to the maturation of the gut barrier at the suckling-to-weaning transition. Targeting the gut microbiota metabolic activity during this key developmental window might therefore be a promising strategy to promote intestinal homeostasis.
Published: 2020
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8. The fecal microbiota of piglets during weaning transition and its association with piglet growth across various farm environments.

Author: Diana Luise, Mathilde Le Sciellour, Arnaud Buchet, Rémi Resmond, Charlène Clement, Marie-Noelle Rossignol, Deborah Jardet, Olivier Zemb, Catherine Belloc, and Elodie Merlot
Subjects: Medicine, Science
Abstract: This study describes the fecal microbiota from piglets reared in different living environments during the weaning transition, and presents the characteristics of microbiota associated with good growth of piglets after weaning. Fecal samples were collected pre- (d26) and post-weaning (d35) from 288 male piglets in 16 conventional indoor commercial farms located in the West of France. The changes one week after weaning on the most abundant microbial families was roughly the same in all farms: alpha diversity increased, the relative abundance of Bacteroidaceae (-61%), Christensenellaceae (-35%), Enterobacteriaceae (-42%), and Clostridiaceae (-32%) decreased, while the relative abundance of Prevotellaceae (+143%) and Lachnospiraceae (+21%) increased. Among all the collected samples, four enterotypes that were ubiquitous in all farms were identified. They could be discriminated by their respective relative abundances of Prevotella, Faecalibacterium, Roseburia, and Lachnospira, and likely corresponded to a gradual maturational shift from pre- to post-weaning microbiota. The rearing environment influenced the frequency of enterotypes, as well as the relative abundance of 6 families at d26 (including Christensenellaceae and Lactobacillaceae), and of 21 families at d35. In all farms, piglets showing the highest relative growth rate during the first three weeks after weaning, which were characterized as more robust, had a higher relative abundance of Bacteroidetes, a lower relative abundance of Proteobacteria, and showed a greater increase in Prevotella, Coprococcus, and Lachnospira in the post-weaning period. This study revealed the presence of ubiquitous enterotypes among the farms of this study, reflecting maturational stages of microbiota from a young suckling to an older cereal-eating profile. Despite significant variation in the microbial profile between farms, piglets whose growth after weaning was less disrupted were, those who had reached the more mature phenotype characterized by Prevotella the fastest.
Published: 2021
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9. Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike‐in standard

Author: Olivier Zemb, Caroline S. Achard, Jerome Hamelin, Marie‐Léa De Almeida, Béatrice Gabinaud, Laurent Cauquil, Lisanne M.G. Verschuren, and Jean‐Jacques Godon
Subjects: 16S rRNA gene, absolute count data, metabarcoding, microbiome, normalization, spike‐in, Microbiology, QR1-502
Abstract: Abstract Metabarcoding of the 16S rRNA gene is commonly used to characterize microbial communities, by estimating the relative abundance of microbes. Here, we present a method to retrieve the concentrations of the 16S rRNA gene per gram of any environmental sample using a synthetic standard in minuscule amounts (100 ppm to 1% of the 16S rRNA sequences) that is added to the sample before DNA extraction and quantified by two quantitative polymerase chain reaction (qPCR) reactions. This allows normalizing by the initial microbial density, taking into account the DNA recovery yield. We quantified the internal standard and the total load of 16S rRNA genes by qPCR. The qPCR for the latter uses the exact same primers as those used for Illumina sequencing of the V3‐V4 hypervariable regions of the 16S rRNA gene to increase accuracy. We are able to calculate the absolute concentration of the species per gram of sample, taking into account the DNA recovery yield. This is crucial for an accurate estimate as the yield varied between 40% and 84%. This method avoids sacrificing a high proportion of the sequencing effort to quantify the internal standard. If sacrificing a part of the sequencing effort to the internal standard is acceptable, we however recommend that the internal standard accounts for 30% of the environmental 16S rRNA genes to avoid the PCR bias associated with rare phylotypes. The method proposed here was tested on a feces sample but can be applied more broadly on any environmental sample. This method offers a real improvement of metabarcoding of microbial communities since it makes the method quantitative with limited efforts.
Published: 2020
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10. Bacterial Consumption of T4 Phages

Author: Jean-Jacques Godon, Ariane Bize, Hoang Ngo, Laurent Cauquil, Mathieu Almeida, Marie-Agnès Petit, and Olivier Zemb
Subjects: bacteriophage, Aeromonas, stable isotope probing, Biology (General), QH301-705.5
Abstract: The bacterial consumption of viruses not been reported on as of yet even though bacteria feed on almost anything. Viruses are widely distributed but have no acknowledged active biocontrol. Viral biomass undoubtedly reintegrates trophic cycles; however, the mechanisms of this phase still remain unknown. 13C-labelled T4 phages monitor the increase of the density of the bacterial DNA concomitant with the decrease of plaque forming units. We used 12C T4 phages as a control. T4 phage disappearance in wastewater sludge was found to occur mainly through predation by Aeromonadacea. Phage consumption also favours significant in situ bacterial growth. Furthermore, an isolated strain of Aeromonas was observed to grow on T4 phages as sole the source of carbon, nitrogen, and phosphorus. Bacterial species are capable of consuming bacteriophages in situ, which is likely a widespread and underestimated type of biocontrol. This assay is anticipated as a starting point for harnessing the bacterial potential in limiting the diffusion of harmful viruses within environments such as in the gut or in water.
Published: 2021
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11. Variability of the Ability of Complex Microbial Communities to Exclude Microbes Carrying Antibiotic Resistance Genes in Rabbits

Author: Caroline Stéphanie Achard, Véronique Dupouy, Suzanne Siviglia, Nathalie Arpaillange, Laurent Cauquil, Alain Bousquet-Mélou, and Olivier Zemb
Subjects: rabbit, gut microbiota, antibiotic resistance gene, 16S sequencing, competitive exclusion, Microbiology, QR1-502
Abstract: Reducing antibiotic use is a necessary step toward less antibiotic resistance in livestock, but many antibiotic resistance genes can persist for years, even in an antibiotic-free environment. In this study, we investigated the potential of three fecal complex microbial communities from antibiotic-naive does to drive the microbiota of kits from antibiotic-exposed dams and outcompete bacteria-carrying antibiotic-resistant genes. The fecal complex microbial communities were either orally delivered or simply added as fresh fecal pellets in four to five nests that were kept clean from maternal feces. Additionally, four nests were cleaned for the maternal feces and five nests were handled according to the common farm practice (i.e., cleaning once a week) as controls. At weaning, we measured the relative abundance of 26 antibiotic resistance genes, the proportion of Enterobacteriaceae resistant to tetracycline and sulfonamide antibiotics, and the taxonomic composition of the microbiota by sequencing the 16S rRNA genes of one kit per nest. Changing the surrounding microbes of the kits can hinder the transmission of antibiotic resistance genes from one generation to the next, but the three communities widely differed in their ability to orient gut microbes and in their impact on antibiotic resistance genes. The most efficient delivery of the microbial community reduced the proportion of resistant Enterobacteria from 93 to 9%, decreased the relative abundance of eight antibiotic resistance genes, and changed the gut microbes of the kits at weaning. The least efficient did not reduce any ARG or modify the bacterial community. In addition, adding fecal pellets was more efficient than the oral inoculation of the anaerobic suspension derived from these fecal pellets. However, we were unable to predict the outcome of the exclusion from the data of the donor does (species composition and abundance of antibiotic resistance genes). In conclusion, we revealed major differences between microbial communities regarding their ability to exclude antibiotic resistance genes, but more work is needed to understand the components leading to the successful exclusion of antibiotic resistance genes from the gut. As a consequence, studies about the impact of competitive exclusion should use several microbial communities in order to draw general conclusions.
Published: 2019
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12. Early Inoculation of Microbial Suspension in Suckling Piglets Affects the Transmission of Maternal Microbiota and the Associated Antibiotic Resistance Genes

Author: Caroline S. Achard, Veronique Dupouy, Laurent Cauquil, Nathalie Arpaillange, Alain Bousquet-Melou, Nathalie Le Floc’h, and Olivier Zemb
Subjects: competitive exclusion, microbiota, piglet, antibiotic resistance genes, Biology (General), QH301-705.5
Abstract: Antibiotic resistance of microbes thriving in the animal gut is a growing concern for public health as it may serve as a hidden reservoir for antibiotic resistance genes (ARGs). We compared 16 control piglets to 24 piglets fed for 3 weeks with S1 or S2 fecal suspensions from two sows that were not exposed to antibiotics for at least 6 months: the first suspension decreased the erythromycin resistance gene ermB and the aminoglycoside phosphotransferase gene conferring resistance to kanamycine (aphA3), while the second decreased the tetracycline resistance gene tetL, with an unexpected increase in ARGs. Using 16S RNA sequencing, we identified microbial species that are likely to carry ARGs, such as the lincosamide nucleotidyltransferase lnuB, the cephalosporinase cepA, and the tetracycline resistance genes tetG and tetM, as well as microbes that never co-exist with the tetracycline resistance gene tetQ, the erythromycin resistance gene ermG and aphA3. Since 73% of the microbes detected in the sows were not detected in the piglets at weaning, a neutral model was applied to estimate whether a microbial species is more important than chance would predict. This model confirmed that force-feeding modifies the dynamics of gut colonization. In conclusion, early inoculation of gut microbes is an interesting possibility to stimulate gut microbiota towards a desirable state in pig production, but more work is needed to be able to predict which communities should be used.
Published: 2020
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13. Microbiota Changes Due to Grape Seed Extract Diet Improved Intestinal Homeostasis and Decreased Fatness in Parental Broiler Hens

Author: Jeremy Grandhaye, Veronique Douard, Ana Rodriguez-Mateos, Yifan Xu, Alex Cheok, Antonella Riva, Rodrigo Guabiraba, Olivier Zemb, Catherine Philippe, Magali Monnoye, Christophe Staub, Eric Venturi, Alix Barbe, Christelle Ramé, Joelle Dupont, and Pascal Froment
Subjects: broiler, grape seed, microbiota, adipose tissue, Biology (General), QH301-705.5
Abstract: In poultry, the selection of broilers for growth performance has induced a deterioration in the health of the parental hens associated with poor reproductive efficiency. To improve these parameters, we administered to laying parental broiler hens a regular diet supplemented or not (Control) with a moderate (1%) or a high level (2%) of grape seed extract (GSE). The 1% GSE diet was administered from a young age (from 4 to 40 weeks of age) and the high level of 2% GSE was administered only during a 2-week period (from 38 to 40 weeks of age) in the laying period. The analysis of 40-week-old hens showed that 2% GSE displayed a reduction in the fat tissue and an improvement in fertility with heavier and more resistant eggs. Seven monomer phenolic metabolites of GSE were significantly measured in the plasma of the 2% GSE hens. GSE supplementation increased the relative abundance of the following bacteria populations: Bifidobacteriaceae, Lactobacilliaceae and Lachnospiraceae. In conclusion, a supplementation period of only 2 weeks with 2% GSE is sufficient to improve the metabolic and laying parameters of breeder hens through a modification in the microbiota.
Published: 2020
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14. Effect of dietary fiber content on nutrient digestibility and fecal microbiota composition in growing-finishing pigs.

Author: Mathilde Le Sciellour, Etienne Labussière, Olivier Zemb, and David Renaudeau
Subjects: Medicine, Science
Abstract: Microbial population in the gastrointestinal tract plays a central role in health and nutrient digestion. The objective of the present study was to investigate the relationships between microbiota and apparent digestibility coefficients with respect to age and diet. Pigs from Large-White, Duroc or Pietrain breeds were raised under the same housing conditions and fed alternately a low-fiber (LF) and a high-fiber diet (HF) during 4 successive 3-week periods. Data collection for digestibility measurements was achieved during the last week of each period. At the end of each period, fecal microbiota was collected for 16S rRNA gene sequencing. The microbiota remained stable across periods whereas digestibility of energy, crude proteins and cell wall components increased. The microbiota was resilient to diet effect and pigs fed the LF diet were discriminated to those fed the HF diet using 31 predicting OTUs with a mean classification error-rate of 3.9%. Clostridiaceae and Turicibacter were negatively correlated whereas Lactobacillus was positively correlated with protein and energy digestibility coefficients in the LF group. In addition, Lachnospiraceae and Prevotella were negatively correlated with cell wall component digestibility. In contrast, no significant correlation was found between microbiota composition and digestibility coefficients when pigs were fed the HF diet. Interestingly, it was also no longer possible to distinguish animals from different breeds once the animals were fed a HF diet, so that the microbiota could only trace the breed origin in the first period and in the LF group. In our experimental conditions, 3 weeks of adaptation to a new diet seems to be sufficient to observe resilience in growing pigs' microbiota. We demonstrated that fecal microbiota can be used to classify pigs according to their dietary treatment. Some bacteria are favorable or unfavorable to digestibility. This suggests that manipulations of bacterial populations can improve digestibility and feed efficiency.
Published: 2018
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15. Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to-weaning transition

Author: Vassilia Theodorou, Helene Eutamene, Cécile Canlet, Céline Barilly, Patrick Aymard, Sylvie Combes, Béatrice Gabinaud, Eloïse Mussard, Sandra Fourre, Charlotte Paës, Corinne Lencina, Roselyne Gautier, Martin Beaumont, Laurent Cauquil, Christelle Knudsen, Olivier Zemb, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Analyse de Xénobiotiques, Identification, Métabolisme (E20 Metatoul-AXIOM), MetaToul-MetaboHUB, Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ToxAlim (ToxAlim), Neuro-Gastroentérologie & Nutrition (ToxAlim-NGN), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), GeT PlaGe, Genotoul (GeT PlaGe), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: 0301 basic medicine, Male, Metabolite, [SDV]Life Sciences [q-bio], RC799-869, Gut flora, chemistry.chemical_compound, Eating, 0302 clinical medicine, RNA, Ribosomal, 16S, solid food, Ingestion, Intestinal Mucosa, Cecum, organoids, biology, digestive, oral, and skin physiology, Gastroenterology, Diseases of the digestive system. Gastroenterology, Cell biology, Animals, Suckling, Infectious Diseases, Milk, [SDV.TOX]Life Sciences [q-bio]/Toxicology, 030211 gastroenterology & hepatology, metabolome, Rabbits, Research Article, Microbiology (medical), Butyrate, Weaning, Microbiology, digestive system, maternal milk, Early life, Permeability, 03 medical and health sciences, In vivo, Metabolome, Organoid, Animals, Humans, intestinal barrier development, Bacteria, Genes, rRNA, biology.organism_classification, Gastrointestinal Microbiome, 030104 developmental biology, chemistry, Gene Expression Regulation, Research Paper/Report, Caco-2 Cells, epithelium, Transcriptome, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Ex vivo
Abstract: International audience; In suckling mammals, the onset of solid food ingestion is coincident with the maturation of the gut barrier. This ontogenic process is driven by the colonization of the intestine by the microbiota. However, the mechanisms underlying the microbial regulation of the intestinal development in early life are not fully understood. Here, we studied the co-maturation of the microbiota (composition and metabolic activity) and of the gut barrier at the suckling-to-weaning transition by using a combination of experiments in vivo (suckling rabbit model), ex vivo (Ussing chambers) and in vitro (epithelial cell lines and organoids). The microbiota composition, its metabolic activity, para-cellular epithelial permeability and the gene expression of key components of the gut barrier shifted sharply at the onset of solid food ingestion in vivo, despite milk was still predominant in the diet at that time. We found that cecal content sterile supernatant (i.e. containing a mixture of metabolites) obtained after the onset of solid food ingestion accelerated the formation of the epithelial barrier in Caco-2 cells in vitro and our results suggested that these effects were driven by the bacterial metabolite butyrate. Moreover, the treatment of organoids with cecal content sterile supernatant partially replicated in vitro the effects of solid food ingestion on the epithelial barrier in vivo. Altogether, our results show that the metabolites produced by the microbiota at the onset of solid food ingestion contribute to the maturation of the gut barrier at the suckling-to-weaning transition. Targeting the gut microbiota metabolic activity during this key developmental window might therefore be a promising strategy to promote intestinal homeostasis.
Published: 2020

16. Gut Microbiota-Derived Metabolite Signature in Suckling and Weaned Piglets

Author: Martin, Beaumont, Laurent, Cauquil, Allan, Bertide, Ingrid, Ahn, Céline, Barilly, Lisa, Gil, Cécile, Canlet, Olivier, Zemb, Géraldine, Pascal, Arnaud, Samson, Sylvie, Combes, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Neovia, Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Analyse de Xénobiotiques, Identification, Métabolisme (E20 Metatoul-AXIOM), MetaToul-MetaboHUB, Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-ToxAlim (ToxAlim), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The present work received the financial support from NEOVIA-ADM., Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse)
Subjects: milk, Swine, animal diseases, [SDV]Life Sciences [q-bio], Weaning, Fatty Acids, Volatile, Animal Feed, metabolomics, Gastrointestinal Microbiome, fluids and secretions, solid food, Pregnancy, RNA, Ribosomal, 16S, Animals, Humans, early life, Female, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: International audience; The gut microbiota plays a key role in intestinal development at the suckling-to-weaning transition. The objective of this study was to analyze the production of metabolites by the gut microbiota in suckling and weaned piglets. We studied piglets raised in two separate maternity farms and weaned at postnatal day 21 in the same farm. The fecal metabolome (1H nuclear magnetic resonance) and the microbiota composition (16S rRNA gene amplicon sequencing) and its predicted functions (PICRUSt2) were analyzed in the same piglets during the suckling period (postnatal day 13) and 2 days after weaning (postnatal day 23). The relative concentrations of the bacterial metabolites methylamine, dimethylamine, cadaverine, tyramine, putrescine, 5-aminovalerate, succinate, and 3-(4-hydroxyphenylpropionate) were higher during the suckling period than after weaning. In contrast, the relative concentrations of the short-chain fatty acids acetate and propionate were higher after weaning than during the suckling period. The maternity of origin of piglets also influenced the level of some bacterial metabolites (propionate and isobutyrate). The fecal metabolome signatures observed in suckling and weaned piglets were associated with specific microbiota-predicted functionalities, structure, and diversity. Gut microbiota-derived metabolites, which are differentially abundant between suckling and weaned piglets (e.g., short-chain fatty acids and biogenic amines), are known to regulate gut health. Thus, identification of metabolome signatures in suckling and weaned piglets paves the way for the development of health-promoting nutritional strategies, targeting the production of bacterial metabolites in early life.
Published: 2021

17. Functional maturation of the gut microbiota at weaning is influenced by maternal environment in piglets

Author: Olivier Zemb, Céline Barilly, Lisa F. Gill, Laurent Cauquil, Géraldine Pascal, Cécile Canlet, Sylvie Combes, Allan Bertide, Ingrid Ahn, Arnaud Samsom, and Martin Beaumont
Subjects: Animal science, fluids and secretions, Ruminococcus, Lactobacillus, animal diseases, Weaning, Microbiome, Biology, Gut flora, biology.organism_classification, Relative species abundance, Feces, Ruminococcaceae
Abstract: SUMMARYThe objective of this study was to analyze in piglets the impact of weaning on the production of metabolites by gut bacteria and to determine whether early life environment influences the functional maturation of the gut microbiota. Fecal metabolome and microbiome were analyzed in piglets raised in two separate maternity farms and mixed at weaning. In piglets from both maternity farms, the relative abundance ofLactobacillusand of the predicted function “Fucose degradation” decreased after weaning while the relative abundance ofRuminococcus 2and of the predicted function “Starch degradation” increased. In piglets from the first maternity farm, the relative concentration of biogenic amines and the relative abundance ofEscherichi-Shigelladecreased after weaning while the relative concentration of short chain fatty acids and the relative abundance ofChristensenellaceae R-7 groupandRuminococcaceae UCG-002increased. These changes were not observed at weaning in piglets from the second maternity farm probably because they already had high relative concentration of short chain fatty acids and higher relative abundance ofChristensenellaceae R-7 groupandRuminococcaceae UCG-002during the suckling period. In conclusion, the functional maturation of the microbiota at weaning is highly dependent on the maternal environment in piglets.ORIGINALITY - SIGNIFICANCE STATEMENTBacterial metabolites are key molecular intermediates between the gut microbiota and host cells. Our study in piglets reveals that the metabolic activity of the gut microbiota shifts at weaning, a key developmental period for intestinal and immune health. We also show that this functional maturation of the gut microbiota is strongly influenced by maternal environment. Thus, targeting early life environmental factors is a promising strategy to program health trough the production of beneficial bacterial metabolites at the suckling-to-weaning transition.
Published: 2020
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18. Early inoculation of microbial suspension in suckling piglets affects the transmission of maternal microbiota and the associated antibiotic resistance genes

Author: Véronique Dupouy, Olivier Zemb, Caroline S. Achard, Nathalie Arpaillange, Alain Bousquet-Mélou, Nathalie Le Floc’h, Laurent Cauquil, Lallemand SAS, Innovations Thérapeutiques et Résistances (InTheRes), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)
Subjects: Microbiology (medical), medicine.drug_class, Tetracycline, Antibiotics, Gut flora, Microbiology, Article, 03 medical and health sciences, Antibiotic resistance, Antibiotic resistance genes, Virology, medicine, Competitive exclusion, lcsh:QH301-705.5, Gene, Feces, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, 030306 microbiology, Inoculation, Piglet, Microbiota, biology.organism_classification, 16S ribosomal RNA, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, lcsh:Biology (General), medicine.drug
Abstract: Antibiotic resistance of microbes thriving in the animal gut is a growing concern for public health as it may serve as a hidden reservoir for antibiotic resistance genes (ARGs). We compared 16 control piglets to 24 piglets fed for 3 weeks with S1 or S2 fecal suspensions from two sows that were not exposed to antibiotics for at least 6 months: the first suspension decreased the erythromycin resistance gene ermB and the aminoglycoside phosphotransferase gene conferring resistance to kanamycine (aphA3), while the second decreased the tetracycline resistance gene tetL, with an unexpected increase in ARGs. Using 16S RNA sequencing, we identified microbial species that are likely to carry ARGs, such as the lincosamide nucleotidyltransferase lnuB, the cephalosporinase cepA, and the tetracycline resistance genes tetG and tetM, as well as microbes that never co-exist with the tetracycline resistance gene tetQ, the erythromycin resistance gene ermG and aphA3. Since 73% of the microbes detected in the sows were not detected in the piglets at weaning, a neutral model was applied to estimate whether a microbial species is more important than chance would predict. This model confirmed that force-feeding modifies the dynamics of gut colonization. In conclusion, early inoculation of gut microbes is an interesting possibility to stimulate gut microbiota towards a desirable state in pig production, but more work is needed to be able to predict which communities should be used.
Published: 2020

19. Transient effect of single or repeated acute deoxynivalenol and zearalenone dietary challenge on fecal microbiota composition in female finishing pigs

Author: David Renaudeau, M. Le Sciellour, Olivier Zemb, Aira Maye Serviento, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Male, 040301 veterinary sciences, [SDV]Life Sciences [q-bio], microbiome, Food Contamination, Biology, SF1-1100, Feed conversion ratio, mycotoxin, 0403 veterinary science, chemistry.chemical_compound, Animal science, RNA, Ribosomal, 16S, Animals, Microbiome, Mycotoxin, Zearalenone, Feces, Nutrition, 2. Zero hunger, acute challenge, Microbiota, 0402 animal and dairy science, swine, 04 agricultural and veterinary sciences, Streptococcaceae, biology.organism_classification, Animal Feed, 040201 dairy & animal science, Diet, Animal culture, chemistry, Female, Animal Science and Zoology, Composition (visual arts), Trichothecenes, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Drug metabolism, performance, Research Article
Abstract: International audience; Mycotoxins are a major contaminant of pig feed and have negative effects on health and performance. The present study investigated the impact of single or repeated acute challenges with a diet naturally contaminated with deoxynivalenol (DON) and zearalenone (ZEN) on growth performances of finishing pigs and their fecal microbiota composition. A total of 160 pigs (castrated males and females) in two successive batches were randomly divided into four experimental groups of 40 pigs each. The control group received a control finisher diet from 99 to 154 days of age. Challenged groups were subjected to a 7-day acute challenge by being fed a DON- and ZEN-contaminated diet (3.02 mg DON/kg feed and 0.76 mg ZEN/kg feed) at 113 days (group DC), 134 days (group CD) or both 113 and 134 days (group DD). Microbiota composition was analyzed via 16S rRNA sequencing from fecal samples collected from the 80 females at 99, 119, 140 and 154 days. Challenged pigs (i.e. groups DC, CD and DD) reduced their average daily feed intake by 25% and 27% ( P < 0.001) and feed efficiency by 34% and 28% ( P < 0.05) during the first and second mycotoxin exposure, respectively. Microbiota composition was affected by mycotoxin exposure ( P = 0.07 during the first exposure and P = 0.01 during the second exposure). At the family level, mycotoxin exposure significantly ( P < 0.05) decreased the relative abundances of Ruminococcaceae, Streptococcaceae and Veillonellaceae and increased that of Erysipelotrichaceae at both 119 and 140 days of age. After the 7-day DON/ZEN challenge, the relative abundance of 6 to 148 operational taxonomic units (OTUs) differed among the treatment groups. However, none of these OTUs changed in all treatment groups. Using 27 functional pathways, pigs exposed to DON/ZEN challenges could be distinguished from control pigs using sparse partial least squares discriminant analysis, with a 15% misclassification rate. Regarding the functionality of these predictors, two pathways were involved in detoxifying mycotoxins: drug metabolism and xenobiotic metabolism by cytochrome P450. In challenged pigs, microbiota composition returned to the initial state within 3 weeks after the end of a single or repeated DON/ZEN challenge, highlighting the resilience of the gut microbiome. The feeding and growth performances of the pigs during challenge periods were significantly correlated with biological pathways related to health problems and modifications in host metabolism. To conclude, short-term DON/ZEN challenges resulted in transient modifications in the composition and functions of fecal microbiota.
Published: 2020

20. Estimating direct genetic and maternal effects affecting rabbit growth and feed efficiency with a factorial design

Author: Hélène Gilbert, Olivier Zemb, Florence Benitez, Elodie Balmisse, Ingrid David, François Richard, Julien Ruesche, Hervé Garreau, L. Drouilhet, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Pôle d'Expérimentation Cunicole TOULousain (PECTOUL ), Institut National de la Recherche Agronomique (INRA), European Project: 633531,H2020,H2020-SFS-2014-2,Feed-a-Gene(2015), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), and Université de Toulouse (UT)-Université de Toulouse (UT)
Subjects: 0301 basic medicine, maternal effect, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Meat, Genotype, growth, Biology, Breeding, Body weight, Weight Gain, Feed conversion ratio, 03 medical and health sciences, Eating, Animal science, Food Animals, feed efficiency, Weaning, Animals, genetics, 2. Zero hunger, Body Weight, 0402 animal and dairy science, Maternal effect, 04 agricultural and veterinary sciences, General Medicine, Factorial experiment, 040201 dairy & animal science, Animal Feed, 030104 developmental biology, Phenotype, residual feed intake, Animal Science and Zoology, Maternal Inheritance, Rabbits, Residual feed intake
Abstract: International audience; The aim of this experiment was to evaluate the significance of neonatal environment on feed efficiency. For that purpose, rabbits from a line selected for residual feed intake (RFI) during 10 generations (G10 kits) were cross-fostered with non-selected control does (i.e., G0 line), and reciprocally. In parallel, sibs were fostered by mothers from their original line. Nine hundred animals were raised in individual (N = 456) or collective (N = 320) cages. Traits analysed in this study were body weight at 32 days and at 63 days, average daily gain (ADG), feed intake between weaning and 63 days (FI), feed conversion ratio (FCR) and RFI. The maternal environment offered by does from the line selected for RFI deteriorated the FCR of the kits, independently of their line of origin, during fattening (+0.08 +/- 0.02) compared to FCR of kits nursed by G0 does. The line, the type of housing and the batch were significant effects for all the measured traits: G10 kits were lighter than their G0 counterparts at 32 days (-82.9 +/- 9 g, p < 0.0001) and at 63 days (-161 +/- 16 g, p < 0.0001). They also had a lower ADG (-2.36 +/- 0.36 g/day, p < 0.0001), RFI (-521 +/- 24 g/day, p < 0.0001) and a lower FI (-855 +/- 31 g, p < 0.0001), resulting in a more desirable feed efficiency (FCR: -0.35 +/- 0.02). There was no significant difference in the contrast of G10 and G0 performances between collective and individual/digestive cages (p > 0.22): -2.35 g/day versus 2.94 g/day for ADG, -0.39 versus -0.40 for FCR, -577 g versus -565 g for RFI and -879 g versus -859 g for FI, respectively). Thus, no genotype-by-environment (housing) interaction is expected at the commercial level, that is, no re-ranking of the animals due to collective housing.
Published: 2019

21. The fecal microbiota of piglets is influenced by the farming environment and is associated with piglet robustness at weaning

Author: Elodie Merlot, Jardet D, Belloc C, Resmond R, Le Sciellour M, Olivier Zemb, Diana Luise, Arnaud Buchet, Clement C, Rossignol M, Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Cooperl Arcatlantique, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de la Recherche Agronomique (INRA), and Sant'Innov
Subjects: food.ingredient, Farming environment, animal diseases, [SDV]Life Sciences [q-bio], Weaning, Coprococcus, 03 medical and health sciences, fluids and secretions, 0302 clinical medicine, Animal science, food, Prevotella, [INFO]Computer Science [cs], Robustness, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Pig, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, Microbiota, Bacteroidetes, biology.organism_classification, Farm environment, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Enterotype, Proteobacteria, Roseburia, 030217 neurology & neurosurgery
Abstract: This study describes the response of piglet microbiota to weaning in various environments, and investigates whether microbiota composition is associated with the robustness of piglets. Faecal samples and growth data were collected just before and 7 days after weaning in 288 piglets from 16 commercial farms characterised by their pathogenic status and antimicrobial use. The effect of weaning on the most abundant microbial families of faecal microbiota was roughly the same in all farms and in agreement with previous findings. Four enterotypes, ubiquitous in all farms, were identified, for which the most discriminating genera werePrevotella,Faecalibacterium,Roseburia, andLachnospira.They corresponded to a gradual maturational shift from pre to post-weaning microbiota. Besides antimicrobial use, the pathogenic status of the farm had a major influence on the post-weaning microbial evolution of apparently healthy piglets. Regarding individual characteristics, piglets whose growth was less perturbed by weaning had moreBacteroidetes(P < 0.01) and lessProteobacteria (P < 0.001).In response to weaning, they showed a greater increase inPrevotella(P < 0.01),Coprococcus(P< 0.01) andLachnospira(P < 0.05) than piglets that grew more slowly. Thus, the microbiota of robust piglets shares common characteristics regardless the living environment of animals.
Published: 2019

22. Effect of gut microbiota on production traits, interaction with genetics

Author: Hélène Gilbert, Sandrine Lagarrigue, Verschuren, L. M. G., Olivier Zemb, Velasco, M., Jean-Luc Gourdine, Bergsma, R., David Renaudeau, Sanchez, J. P., Hervé Garreau, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Topigs Norsvin Research Center B.V., Schoenaker, Partenaires INRAE, Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Unité de Recherches Zootechniques (URZ), Institut National de la Recherche Agronomique (INRA), European Union’s H2020 Feed-a-Gene Project (grant 633531, European Project: 633531,H2020,H2020-SFS-2014-2,Feed-a-Gene(2015), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institute of Agrifood Research and Technology (IRTA)
Subjects: pig, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, gut microbiota, [SDV]Life Sciences [q-bio], rabbit, microbiability, feed efficiency, [INFO]Computer Science [cs], digestive system
Abstract: International audience; Gut microbiota is a key contributor to feed use in monogastric species, in particular via the digestion dietary fibres. Molecular techniques are now available to run large studies and decipher the potential of gut microbiota to improve livestock. Studies on human and mice are more advanced: different factors have been demonstrated to influence the gut microbiota composition and functions, including maternal transmission, environment (diet composition and quantity, humidity and heat), age and physiological status. Studies also evaluated if the host controls its gut microbiota. In pigs, chicken and rabbits, microbiota differences between animals of extreme phenotypes within populations, and between lines divergently selected for specific traits, are reported. Other studies reported that some microbiota abundancies are heritable. Linear mixed models have been used to evaluate its contribution to trait variability, or microbiability, with different data (full vs 16S sequencing of gut or faecal contents) and different variance matrices. They showed significant contribution to production traits, reaching more than 30%. However, confounding effects exist, such as the maternal inheritance of the microbiota and the genetic determinism by the host : many studies show reduction of the genetic additive variance, in addition to reduction of the residual variance with microbiability. Specific datasets, testing a given genetic in different environments or using cross-fostering, are used to better understand the relative contribution of each effect (host genetics and microbiota) to the trait variance, and propose solutions to livestock.
Published: 2018

23. Corrigendum: Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex

Author: Hélène Gilbert, Alfons J. M. Jansman, Mario P. L. Calus, Lisanne M G Verschuren, Olivier Zemb, Egbert F. Knol, and R. Bergsma
Subjects: 0301 basic medicine, Animal Nutrition, 0402 animal and dairy science, Microbial composition, 04 agricultural and veterinary sciences, General Medicine, Biology, Animal Breeding and Genomics, 040201 dairy & animal science, Feed conversion ratio, Diervoeding, 03 medical and health sciences, 030104 developmental biology, Variation (linguistics), Genetics, WIAS, Life Science, Animal Science and Zoology, Fokkerij en Genomica, Food science, Fokkerij & Genomica, Feces, Food Science, Animal Breeding & Genomics
Published: 2018

24. Effect of dietary fiber content on nutrient digestibility and fecal microbiota composition in growing-finishing pigs

Author: Olivier Zemb, Mathilde Le Sciellour, Etienne Labussière, David Renaudeau, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, European Project: 633531,H2020,H2020-SFS-2014-2,Feed-a-Gene(2015), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), and Université de Toulouse (UT)-Université de Toulouse (UT)
Subjects: 0301 basic medicine, Dietary Fiber, Male, Swine, Surfactants, Population Dynamics, lcsh:Medicine, Pathology and Laboratory Medicine, Feces, Lactobacillus, RNA, Ribosomal, 16S, Prevotella, Medicine and Health Sciences, lcsh:Science, Materials, 2. Zero hunger, Mammals, education.field_of_study, Multidisciplinary, biology, Organic Compounds, Microbiota, Eukaryota, Genomics, population bactérienne, Breed, Bacterial Pathogens, Chemistry, Medical Microbiology, Alimentation et Nutrition, Vertebrates, Physical Sciences, efficience alimentaire, Animal Nutritional Physiological Phenomena, Digestion, Cellular Structures and Organelles, Pathogens, Research Article, digestibilité, Population, Materials Science, Detergents, Microbial Genomics, Feed conversion ratio, Microbiology, 03 medical and health sciences, Animal science, Cell Walls, microbiote, Genetics, Food and Nutrition, Animals, nutrition animale, education, Cellulose, Microbial Pathogens, Nutrition, Clostridium, Bacteria, Lachnospiraceae, Organic Chemistry, Gut Bacteria, lcsh:R, Organisms, Chemical Compounds, Biology and Life Sciences, Nutrients, Sequence Analysis, DNA, Cell Biology, biology.organism_classification, Diet, 030104 developmental biology, Amniotes, lcsh:Q, Microbiome, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, porc
Abstract: International audience; Microbial population in the gastrointestinal tract plays a central role in health and nutrient digestion. The objective of the present study was to investigate the relationships between microbiota and apparent digestibility coefficients with respect to age and diet. Pigs from Large-White, Duroc or Pietrain breeds were raised under the same housing conditions and fed alternately a low-fiber (LF) and a high-fiber diet (HF) during 4 successive 3-week periods. Data collection for digestibility measurements was achieved during the last week of each period. At the end of each period, fecal microbiota was collected for 16S rRNA gene sequencing. The microbiota remained stable across periods whereas digestibility of energy, crude proteins and cell wall components increased. The microbiota was resilient to diet effect and pigs fed the LF diet were discriminated to those fed the HF diet using 31 predicting OTUs with a mean classification error-rate of 3.9%. Clostridiaceae and Turicibacter were negatively correlated whereas Lactobacillus was positively correlated with protein and energy digestibility coefficients in the LF group. In addition, Lachnospiraceae and Prevotella were negatively correlated with cell wall component digestibility. In contrast, no significant correlation was found between microbiota composition and digestibility coefficients when pigs were fed the HF diet. Interestingly, it was also no longer possible to distinguish animals from different breeds once the animals were fed a HF diet, so that the microbiota could only trace the breed origin in the first period and in the LF group. In our experimental conditions, 3 weeks of adaptation to a new diet seems to be sufficient to observe resilience in growing pigs' microbiota. We demonstrated that fecal microbiota can be used to classify pigs according to their dietary treatment. Some bacteria are favorable or unfavorable to digestibility. This suggests that manipulations of bacterial populations can improve digestibility and feed efficiency.
Published: 2018

25. Impact of feed restriction and housing hygiene conditions on specific and inflammatory immune response, the cecal bacterial community and the survival of young rabbits

Author: Océane C B Martin, Sylvie Combes, K. Massip, Géraldine Pascal, Olivier Zemb, Thierry Gidenne, Isabelle P. Oswald, O. Bouchez, N. Le Floc’h, Laurent Cauquil, H. Furbeyre, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], INPT-ENSAT - INPT-ENVT, UMR 1388 GenPhySE Génétique Physiologie et Systèmes d'Elevage., Institut National de la Recherche Agronomique (INRA), ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), GeT PlaGe, Genotoul, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Biosynthèse & Toxicité des Mycotoxines (ToxAlim-BioToMyc), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, Institut National de la Recherche Agronomique ( INRA ), Toxalim, Université de Toulouse, INRA, INPT, ENVT, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] ( PEGASE ), Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ProdInra, Archive Ouverte, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Male, specific and inflammatory immune response, Veterinary medicine, Globulin, media_common.quotation_subject, [SDV]Life Sciences [q-bio], rabbit, housing hygiene, Feed conversion ratio, SF1-1100, feed restriction, 03 medical and health sciences, Animal science, Immune system, Hygiene, medicine, Weaning, Animals, cecal microbiota, media_common, Caloric Restriction, 2. Zero hunger, biology, [ SDV ] Life Sciences [q-bio], business.industry, Lachnospiraceae, Haptoglobin, 0402 animal and dairy science, 04 agricultural and veterinary sciences, Feeding Behavior, 040201 dairy & animal science, Housing, Animal, Immunity, Innate, Gastrointestinal Microbiome, Animal culture, [SDV] Life Sciences [q-bio], 030104 developmental biology, biology.protein, Animal Science and Zoology, Female, Rabbits, medicine.symptom, business, Weight gain
Abstract: Limiting the post-weaning intake of the young rabbit is known to improve its resistance to digestive disorders, whereas a degradation of its housing hygiene is assumed to have a negative impact on its health. This study aims at providing insights into the mechanism of digestive health preservation regarding both host (growth and immune response) and its symbiotic digestive microbiota. A 2×2 factorial design from weaning (day 28) to day 64 was set up: ad libitum intake or restricted intake at 70% of ad libitum, and high v. low hygiene of housing (n=105 per group). At day 36 and day 45, 15 animals/group were subcutaneously immunized with ovalbumin (OVA) to assess their specific immune response. Blood was sampled at 36, 45, 57 and 64 days of age to determine total and anti-OVA immunoglobulin type G (IgG) and haptoglobin levels. The cecal bacterial community was explored (18 per group) by 454 pyrosequencing of genes coding for the 16S ribosomal RNA, whereas cecal pH, NH3 and volatile fatty acid (VFA) concentrations were measured to characterize fermentative activity. A 30% reduction in feed intake reduced the growth by only 17% (P
Published: 2017

26. Role of the metacommunity in the colonization of rabbit's intestinal tract to fight against antibiotic-resistant bacteria

Author: Caroline Achard, Beatrice Gabinaud, Sylvie Combes, Véronique Dupouy, Yuliaxis Ramayo Caldas, Catherine Denis, Maria Ballester, Nathalie Le Floch, Samuel Boucher, Stéphane Chatellier, Bernadette Le Normand, Alain Bousquet-Mélou, Jordi Estellé, Olivier Zemb, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, ToxAlim (ToxAlim), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), LABOVET Conseil, Réseau Cristal, Clinique Vétérinaire des Marchés de Bretagne, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, antibiotic-intestinal, [SDV]Life Sciences [q-bio], rabbit, microbiota, [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2016

27. Impact of feed restriction on health, digestion and faecal microbiota of growing pigs housed in good or poor hygiene conditions

Author: N. Le Floc’h, Lucile Montagne, Olivier Zemb, Elodie Merlot, C. Knudsen, Thierry Gidenne, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Tissus animaux, nutrition, digestion, écosystème et métabolisme (TANDEM), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-INP. Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, UMR 1289 TANDEM, Ecole Nationale Supérieure Agronomique de Toulouse, Ecole Nationale Vétérinaire de Toulouse (ENVT), Université européenne de Bretagne - European University of Brittany (UEB), CI PHASE, AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT], and Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST
Subjects: Male, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Veterinary medicine, condition d'élevage, Swine, Weight Gain, feed restriction, Feces, Faecal consistency, Hygiene, Phylogeny, media_common, 2. Zero hunger, Animal biology, 0303 health sciences, Microbiota, [SDV.BA]Life Sciences [q-bio]/Animal biology, pigs, 04 agricultural and veterinary sciences, Housing, Animal, Animal culture, Agricultural sciences, restriction alimentaire, Animal Nutritional Physiological Phenomena, Digestion, Female, medicine.symptom, Animal feed, media_common.quotation_subject, growth, Weaning, Biology, Feed conversion ratio, SF1-1100, DNA, Ribosomal, hygiène, 03 medical and health sciences, microbiote, Biologie animale, medicine, croissance animale, Animals, 030304 developmental biology, 0402 animal and dairy science, Sequence Analysis, DNA, 040201 dairy & animal science, Animal Feed, Animal Science and Zoology, Weight gain, Sciences agricoles, porc
Abstract: Feed restriction could be a relevant strategy to preserve gut health, reduce systemic inflammatory response and finally limit antibiotic use. This study assessed the effect of feed restriction on growing pigs submitted to a moderate inflammatory challenge induced by the degradation of the environmental hygiene that is known to alter growth rate. The experiment was run on 80 pigs selected at 7 weeks of age according to a 2×2 factorial design: two feeding levels, ad libitum (AL) and feed restricted (FR) at 60% of AL, and two conditions of environmental hygiene, clean and dirty. Pigs were housed individually throughout the experiment. From 61 to 68 days of age (day 0 to 7), pigs were housed in a post weaning unit and feed restriction was applied to half of the pigs from day 0 to day 29. At 68 days of age (day 7 of the experiment), pigs were transferred in a growing unit where half of FR and half of AL pigs were housed in a dirty environment (poor hygiene) and the other half in a clean environment (good hygiene) until day 42. Growth performance was recorded weekly. Blood and faeces samples were collected to measure indicators of inflammation, nutrient digestibility and microbiota composition. Faecal consistency was monitored daily to detect diarrhoeas. Feed restriction decreased daily weight gain (-35% to -50%, P
Published: 2014

28. Complete chloroform dechlorination by organochlorine respiration and fermentation

Author: Matthew, Lee, Adrian, Low, Olivier, Zemb, Joanna, Koenig, Astrid, Michaelsen, Mike, Manefield, University of New South Wales [Sydney] (UNSW), Tissus animaux, nutrition, digestion, écosystème et métabolisme (TANDEM), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]
Subjects: Methylene Chloride, Halogenation, [SDV]Life Sciences [q-bio], mixed culture, dehalococcoide, dichloromethane, carbon-tetrachloride, dechlorination, Biodegradation, Environmental, Peptococcaceae, Fermentation, Hydrocarbons, Chlorinated, dehalobacterium-formicoaceticum, reductive, [INFO]Computer Science [cs], Chloroform, sp-nov, enrichment culture, vinyl-chloride, Soil Microbiology, Hydrogen, degradation
Abstract: International audience; Chloroform (CF, CHCl3) is a recalcitrant and toxic environmental pollutant. In this communication we report for the first time a microbial community capable of complete CF dechlorination by metabolic processes. Cultures derived from subsurface soil (3.5 m) could sustain complete dechlorination of CF at levels of least 360 mu M at a rate of 40 mu M per day. Scrutiny of CF dechlorination revealed two metabolic processes at work. First, CF was respired to dichloromethane (DCM, CH2Cl2), which was then fermented to acetate, hydrogen and carbon dioxide. Elevated hydrogen partial pressures were found to inhibit the fermentation process. Interspecies hydrogen transfer was observed in the form of methanogenesis and acetogenesis. This suggests that the dechlorination process required syntrophic partners to maintain low hydrogen partial pressures. C-13-labelled DCM was employed to help elucidate the chemistry of the process and identify bacterial community members involved. CF respiring cultures, where emulsified vegetable oil was supplied as the electron donor and DCM fermenting cultures, where DCM was supplied as the sole organic carbon source were studied separately. Pyrosequencing of these cultures revealed Dehalobacter lineages as a predominant community member in both. Subsequent growth experiments confirmed that the proliferation of Dehalobacter was linked directly to both the dehalorespiration and dehalofermentation processes.
Published: 2012

29. Direct rRNA fingerprinting, a novel method to profile low diversity microbial communities

Author: Olivier Zemb, Maria-Luisa Gutierrez-Zamora, Mike Manefield, University of New South Wales [Sydney] (UNSW), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: DNA, Bacterial, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Soil Science, Fresh Water, Biology, dna, 03 medical and health sciences, Microbial ecology, Abundance (ecology), RNA, Ribosomal, 16S, bacterial, [INFO]Computer Science [cs], cleavage, activated-sludge, Relative species abundance, Ecosystem, Phylogeny, Ecology, Evolution, Behavior and Systematics, sscp, 030304 developmental biology, 0303 health sciences, Bacteria, Ecology, 030306 microbiology, Community structure, Biodiversity, Ribosomal RNA, 16S ribosomal RNA, DNA Fingerprinting, Bacterial Typing Techniques, Microbial population biology, phenolic-compound, Evolutionary biology, Community Fingerprinting
Abstract: International audience; In the past decade, an increasing number of methods in microbial ecology have been developed that address the questions of which microbes exist in the environment, what their roles are and, to some extent, what their abundance is. In the present paper, we propose and describe the proof of principle of a novel method for analysing shifts in microbial community composition that uses small RNA fragments directly derived from 16S rRNA. Community fingerprints are generated on the basis of sequence-dependent conformational differences of rRNA fragments. We applied this method to profile artificial and natural communities and to detect changes in community structure in enrichment cultures. This method constitutes a PCR-free alternative to microbial community characterisation and can provide information on the relative abundance of rRNA from individual phylotypes in low diversity samples.
Published: 2011

30. Reactive iron barriers: a niche enabling microbial dehalorespiration of 1,2-dichloroethane

Author: Olivier Zemb, Adrian F. Low, Matthew Lee, Mike Manefield, Tissus animaux, nutrition, digestion, écosystème et métabolisme (TANDEM), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT], and University of New South Wales [Sydney] (UNSW)
Subjects: Hydrogen, Environmental remediation, Iron, Microorganism, [SDV]Life Sciences [q-bio], chemistry.chemical_element, Dehalobacter, 010501 environmental sciences, 1,2-Dichloroethane, 01 natural sciences, Applied Microbiology and Biotechnology, 03 medical and health sciences, chemistry.chemical_compound, [INFO]Computer Science [cs], Anaerobiosis, Ethylene Dichlorides, 0105 earth and related environmental sciences, 0303 health sciences, Zerovalent iron, Bacteria, biology, 030306 microbiology, Chemistry, Biodiversity, General Medicine, Ethylenes, Hydrogen-Ion Concentration, biology.organism_classification, 6. Clean water, Microbial population biology, Environmental chemistry, Chlorine, Water Microbiology, Groundwater, Biotechnology
Abstract: International audience; A reactive iron barrier in a contaminated aquifer with low pH was found to dechlorinate 1,2-dichloroethane (1,2-DCA) in situ. This chlorinated ethane is known to resist abiotic reduction by zero valent iron. Samples taken up-gradient and within the barrier were used to inoculate anaerobic batch cultures amended with various electron donors. Cultures inoculated with groundwater from within the reactive iron barrier reduced 1,2-DCA to ethene. The same effect could be achieved by simultaneously supplying hydrogen while neutralising pH. The presence of iron or hydrogen at neutral pH had negligible effects on 1,2-DCA reduction in cultures inoculated with groundwater sampled up-gradient of the barrier. Molecular microbial community characterisation revealed that Dehalobacter species were more abundant in groundwater sampled from within the barrier. These findings suggest reactive iron barriers represent a remediation technology for 1,2-DCA degradation acting through in situ recruitment of 1,2-DCA reducing bacteria such as Dehalobacter.
Published: 2010

31. Efficient method to isolate and purify viruses of bacteria from marine environments

Author: Olivier Zemb, L. Urios, Clémence Coetsier, Philippe Lebaron, Université Pierre et Marie Curie - Paris 6 (UPMC), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Observatoire Océanologique
Subjects: viruses, [SDV]Life Sciences [q-bio], water, Environment, Applied Microbiology and Biotechnology, Virus, Microbiology, 03 medical and health sciences, bacteriophage, Yeast extract, Bacteriophages, Seawater, north-sea, 030304 developmental biology, 0303 health sciences, Bacteria, biology, 030306 microbiology, Host (biology), Inoculation, genetic diversity, Isolation (microbiology), biology.organism_classification, Virology, hawaii, Lytic cycle, Water Microbiology
Abstract: Aim: To isolate viruses of specific heterotrophic bacterial strains from marine environments using a host addition/virus amplification protocol (HAVAP) for use in phage/host systems. Methods and Results: Bacteria-free seawater samples containing natural viruses assemblages were inoculated with a single laboratory grown bacterial host of interest in a nutrient-enriched [peptone, Fe(III) and yeast extract] seawater suspension. These conditions enhanced the replication of only those virus(s) capable of infecting the host bacterium. After incubation, free viruses were recovered at concentrations ranging 105–1010 infectious virus particles per ml of seawater. Using this approach, 15 viruses were isolated and represented 12 unique phage/host systems. Two of the hosts tested were infected by more than one virus. Conclusions: Isolation of high concentrations of specific viruses is possible even if their initial concentrations in native waters are low. This approach allows the recovery of phage/host systems that may not be numerically dominant. Significance and Impact of the Study: This host enrichment protocol for virus detection and isolation is well-suited for aquatic viral ecology studies that require phage/host systems.
Published: 2008

32. Safum: statistical analysis of SSCP fingerprints using PCA projections, dendrograms and diversity estimators

Author: Olivier Zemb, Philippe Lebaron, Jean-Jacques Godon, Bart Haegeman, Jean Philippe Delgenes, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Pierre et Marie Curie - Paris 6 (UPMC), Water Resource Modeling (MERE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)
Subjects: DIVERSITY, MICROBIAL, Biology, Bioinformatics, Biochemistry, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, CAPILLARY ELECTROPHORESIS, Statistical analysis, FINGERPRINT, 030304 developmental biology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Ecology, BIOCHIMIE, 030306 microbiology, business.industry, Dendrogram, Fingerprint (computing), Estimator, Pattern recognition, Single-strand conformation polymorphism, STATISTICAL ANALYSIS, BIOLOGIE MOLECULAIRE, SSCP, Euclidean distance, Principal component analysis, Artificial intelligence, business
Abstract: International audience; The program safum provides a smart interface to import, visualize and compare fingerprinting profiles, especially on capillary electrophoresis single strand conformation polymorphism data, in conjunction with basic statistical analysis tools. It includes principal component analysis, two- or three-dimensional representations, dendrograms based on Euclidean distance, and easily exportable files for subsequent applications. safum is useful for the analysis of spatial or temporal sequences of microbial community fingerprints obtained with an ABI prism sequencer.
Published: 2007

33. Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity

Author: Claude Lobry, Patrice Loisel, Eric Latrille, Jérôme Harmand, Olivier Zemb, Jean Philippe Delgenes, Jean-Jacques Godon, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Water Resource Modeling (MERE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)
Subjects: DNA, Bacterial, Swine, Microbial diversity, In silico, Biology, Microbiology, Feces, 03 medical and health sciences, Microbial ecosystem, DENATURING GRADIENT ELECTROPHORESIS, Animals, Polymorphism, Single-Stranded Conformational, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, SINGLE STRAND CONFORMATION POLYMORPHISM, Bacteria, 030306 microbiology, Single-strand conformation polymorphism, respiratory system, DNA Fingerprinting, Molecular biology, Electrophoresis, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Evolutionary biology, Data Interpretation, Statistical, Log-normal distribution, Electrophoresis, Polyacrylamide Gel, human activities
Abstract: Summary The exact extent of microbial diversity remains unknowable. Nevertheless, fingerprinting patterns (denaturing gradient electrophoresis (DGE), single- strand conformation polymorphism (SSCP)) provide an image of a microbial ecosystem and contain diversity data. We generated numerical simulation fingerprinting patterns based on three types of distribution (uniform, geometric and lognormal) with a range of units from 10 to 500 000. First, simulated patterns containing a diversity of around 1000 units or more gave patterns similar to those obtained in experiments. Second, the number of bands or peaks saturated quickly to about 35 and were unrelated to the degree of diversity. Finally, assuming lognormal distribution, we used an estimator of diversity on in silico and experimental fingerprinting patterns. Results on in silico patterns corresponded to the sim- ulation inputs. Diversity results in experimental pat- terns were in the same range as those obtained from the same DNA sample in molecular inventories. Thus, fingerprinting patterns contain extractable data about diversity although not on the basis of a number of bands or peaks, as is generally assumed to be the case.
Published: 2006

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33 results on '"Olivier Zemb"'

1. The transplantation of the gut microbiome of fat-1 mice protects against colonic mucus layer disruption and endoplasmic reticulum stress induced by high fat diet

2. The potential of microbiota information to better predict efficiency traits in growing pigs fed a conventional and a high-fiber diet

3. Genome wide association study of growth and feed efficiency traits in rabbits

4. Gut microbiota and host genetics contribute to the phenotypic variation of digestive and feed efficiency traits in growing pigs fed a conventional and a high fiber diet

5. Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs

6. Chronic dietary exposure to a glyphosate-based herbicide results in total or partial reversibility of plasma oxidative stress, cecal microbiota abundance and short-chain fatty acid composition in broiler hens

7. Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to-weaning transition

8. The fecal microbiota of piglets during weaning transition and its association with piglet growth across various farm environments.

9. Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike‐in standard

10. Bacterial Consumption of T4 Phages

11. Variability of the Ability of Complex Microbial Communities to Exclude Microbes Carrying Antibiotic Resistance Genes in Rabbits

12. Early Inoculation of Microbial Suspension in Suckling Piglets Affects the Transmission of Maternal Microbiota and the Associated Antibiotic Resistance Genes

13. Microbiota Changes Due to Grape Seed Extract Diet Improved Intestinal Homeostasis and Decreased Fatness in Parental Broiler Hens

14. Effect of dietary fiber content on nutrient digestibility and fecal microbiota composition in growing-finishing pigs.

15. Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to-weaning transition

16. Gut Microbiota-Derived Metabolite Signature in Suckling and Weaned Piglets

17. Functional maturation of the gut microbiota at weaning is influenced by maternal environment in piglets

18. Early inoculation of microbial suspension in suckling piglets affects the transmission of maternal microbiota and the associated antibiotic resistance genes

19. Transient effect of single or repeated acute deoxynivalenol and zearalenone dietary challenge on fecal microbiota composition in female finishing pigs

20. Estimating direct genetic and maternal effects affecting rabbit growth and feed efficiency with a factorial design

21. The fecal microbiota of piglets is influenced by the farming environment and is associated with piglet robustness at weaning

22. Effect of gut microbiota on production traits, interaction with genetics

23. Corrigendum: Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex

24. Effect of dietary fiber content on nutrient digestibility and fecal microbiota composition in growing-finishing pigs

25. Impact of feed restriction and housing hygiene conditions on specific and inflammatory immune response, the cecal bacterial community and the survival of young rabbits

26. Role of the metacommunity in the colonization of rabbit's intestinal tract to fight against antibiotic-resistant bacteria

27. Impact of feed restriction on health, digestion and faecal microbiota of growing pigs housed in good or poor hygiene conditions

28. Complete chloroform dechlorination by organochlorine respiration and fermentation

29. Direct rRNA fingerprinting, a novel method to profile low diversity microbial communities

30. Reactive iron barriers: a niche enabling microbial dehalorespiration of 1,2-dichloroethane

31. Efficient method to isolate and purify viruses of bacteria from marine environments

32. Safum: statistical analysis of SSCP fingerprints using PCA projections, dendrograms and diversity estimators

33. Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity

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33 results on '"Olivier Zemb"'

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