Yuliaxis Ramayo-Caldas

Yuliaxis Ramayo-Caldas
French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE · Department of Animal Genetics

Ramon y Cajal Research Contract

About

194
Publications
23,763
Reads
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2,021
Citations
Additional affiliations
January 2014 - present
French National Institute for Agriculture, Food, and Environment (INRAE)
Position
  • Junior Research Scientist
August 2013 - present
French National Institute for Agriculture, Food, and Environment (INRAE)
Position
  • Postdoctoral AgreenSkills
January 2012 - July 2013
CRAG Centre for Research in Agricultural Genomics
Position
  • PhD Student

Publications

Publications (194)
Article
Full-text available
Background The rabbit cecum hosts and interacts with a complex microbial ecosystem that contributes to the variation of traits of economic interest. Although the influence of host genetics on microbial diversity and specific microbial taxa has been studied in several species (e.g., humans, pigs, or cattle), it has not been investigated in rabbits....
Conference Paper
Full-text available
El ciego del conejo alberga la comunidad microbiana más rica y diversa de su tracto gastrointestinal que influye sobre las condiciones ambientales de este órgano y sobre la disponibilidad de nutrientes del hospedador. Esta relación simbiótica hospedador-microbiota sugiere una adaptación evolutiva mutua que promovería el crecimiento de aquellos micr...
Conference Paper
Full-text available
The aim of this study was to identify the regions involved in the genetic control of the composition of different microbial communities present in the rabbit cecum. The available material consisted of the genotypes (~200K SNPs) and a set of microbial traits representative of the cecal microbiota of 412 rabbits. Two approaches were used to identify...
Article
In this study we used the phenotypic information of 1,499 Duroc pigs, recorded longitudinally in the age period from 110 to 200 days of age for individual daily feed intake (DFI), backfat thickness (BF) and live body weight (BW). Our aim was to estimate the genetic parameters for production and feed efficiency traits during the fattening period, wi...
Article
Full-text available
Weaning is a critical period in the life of pigs with repercussions on their health and welfare and on the economy of the swine industry. This study aimed to assess the effect of the commercial early weaning on gut microbiota, intestinal gene expression and serum metabolomic response via an integrated-omic approach combining 16S rRNA gene sequencin...
Article
Full-text available
Background In the early 20th century, Cuban farmers imported Charolais cattle (CHFR) directly from France. These animals are now known as Chacuba (CHCU) and have become adapted to the rough environmental tropical conditions in Cuba. These conditions include long periods of drought and food shortage with extreme temperatures that European taurine ca...
Article
Full-text available
Background Analysis and prediction of complex traits using microbiome data combined with host genomic information is a topic of utmost interest. However, numerous questions remain to be answered: how useful can the microbiome be for complex trait prediction? Are estimates of microbiability reliable? Can the underlying biological links between the h...
Article
Full-text available
In recent years, the increase in awareness of antimicrobial resistance together with the societal demand of healthier meat products have driven attention to health-related traits in livestock production. Previous studies have reported medium to high heritabilities for these traits and described genomic regions associated with them. Despite its gene...
Conference Paper
Full-text available
Selecting for feed efficiency (FE) is challenging in rabbit breeding programs since individual feed intake (FI) of animals is not usually available. The current study raises the possibility that rabbits' cecal microbiota could be considered to predict FE and its component traits, i.e., growth and FI. Our dataset comprised the individual average dai...
Article
Full-text available
Background The gut microbiota influences host performance playing a relevant role in homeostasis and function of the immune system. The aim of the present work was to identify microbial signatures linked to immunity traits and to characterize the contribution of host-genome and gut microbiota to the immunocompetence in healthy pigs. Results To ach...
Poster
Full-text available
Rabbit cecum hosts and constantly interacts with a complex microbial ecosystem that contributes to the variation of traits of economic interest. The heritability of the abundances of these microorganisms remains unknown but previous studies in humans, pigs, or cattle have reported moderate heritabilities for specific microbial taxa. This study repo...
Article
Full-text available
Gut microbiota plays an important role in nutrient absorption and could impact rabbit feed efficiency. This study aims at investigating such impact by evaluating the value added by microbial information for predicting individual growth and cage phenotypes related to feed efficiency. The dataset comprised individual average daily gain and cage-avera...
Preprint
Full-text available
Bulk sequencing of RNA transcripts has typically been used to quantify gene expression levels and regulatory signals in different experimental systems. However, linking differentially expressed (DE) mRNA transcripts to gene expression regulators, such as miRNAs, remains challenging, as miRNA-mRNA interactions are commonly identified post hoc after...
Preprint
Full-text available
The aim of the present work was to identify microbial biomarkers linked to immunity traits and to characterize the contribution of host-genome and gut microbiota to the immunocompetence in healthy pigs. To achieve this goal, we undertook a combination of network, mixed model and microbial-wide association studies (MWAS) for 21 immunity traits and t...
Article
Full-text available
Ruminants, like all mammals, are home to trillions of symbiotic microbes that constitute the microbiota of the skin, digestive, respiratory and genital tracts. The composition and functions of these microbes depend, among other things, on their habitat. The use of omic approaches, in particular new-generation sequencing, has made it possible to cha...
Preprint
Full-text available
Gut microbiota plays an important role in nutrient absorption and could impact rabbit feed efficiency. This study aims at investigating such impact by evaluating the value added by microbial information for predicting individual growth and cage phenotypes related to feed efficiency. The dataset comprised individual average daily gain and cage-avera...
Article
Les ruminants, comme tous les mammifères, hébergent des billions de microbes symbiotiques, constituant les « microbiotes » de la peau, des voies digestives, respiratoires et génitales etc. La composition et les fonctions de ces microbiotes dépendent, entre autres, de leur habitat. L’utilisation des approches « -omiques », en particulier le séquença...
Article
Full-text available
The aim of this study was to determine the possible impact of early socialization and an enriched neonatal environment to improve adaptation of piglets to weaning. We hypothesized that changes in the microbiota colonization process and in their metabolic response and intestinal functionality could help the animals face weaning stress. A total of 48...
Article
Full-text available
Essential oils (EOs) are promising alternatives to chemotherapeutics in animal production due to their immunostimulant, antimicrobial, and antioxidant properties, without associated environmental or hazardous side effects. In the present study, the modulation of the transcriptional immune response (microarray analysis) and microbiota [16S Ribosomal...
Article
Full-text available
Background: Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical "single-gene-single-trait" approaches and have evaluated...
Article
Full-text available
The advent of next-generation sequencing technologies allowed relative quantification of microbiome communities and their spatial and temporal variation. In recent years, supervised learning (i.e., prediction of a phenotype of interest) from taxonomic abundances has become increasingly common in the microbiome field. However, a gap exists between s...
Article
Full-text available
Background French beef producers suffer from the decrease in profitability of their farms mainly because of the continuous increase in feed costs. Selection for feed efficiency in beef cattle represents a relevant solution to face this problem. However, feed efficiency is a complex trait that can be assessed by three major criteria: residual feed i...
Article
Full-text available
Background Genetic pressure in animal breeding is sparking the interest of breeders for selecting elite boars with higher sperm quality to optimize ejaculate doses and fertility rates. However, the molecular basis of sperm quality is not yet fully understood. Our aim was to identify candidate genes, pathways and DNA variants associated to sperm qua...
Article
Full-text available
Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity...
Conference Paper
Full-text available
Aiming to study the effect of different management factors on rabbit cecal microbial composition and diversity, a 16S rDNA-based assessment through MiSeq platform was performed. Cecal samples were collected from 425 rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with food supplemented or free of...
Article
Full-text available
The inclusion of health-related traits, or functionally associated genetic markers, in pig breeding programs could contribute to produce more robust and disease resistant animals. The aim of the present work was to study the genetic determinism and genomic regions associated to global immunocompetence and health in a Duroc pig population. For this...
Poster
Full-text available
Rabbit cecum harbors a complex microbial ecosystem whose members constantly interact between them and with their host to ensure homeostatic balance maintenance. Our objective was to estimate heritability of rabbit cecal microbiota in order to assess whether interactions with the host also occur at genetic level. 16S rDNA amplicon MiSeq sequencing w...
Poster
Full-text available
Microbial communities inhabiting gastrointestinal tract are expected to affect animal growth and feed efficiency given their well-known role in nutrient absorption and immunological processes. Our objective was to assess whether predictive ability of linear models for growth (G) and cage feed intake (FI) and feed conversion ratio (FCR) is improved...
Article
Full-text available
Background: The effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the leve...
Preprint
Full-text available
The analysis and prediction of complex traits using microbiome data combined with host genomic information is a topic of utmost interest. However, numerous questions remain to be answered: How useful can the microbiome be for complex trait prediction? Are microbiability estimates reliable? Can the underlying biological links between the host’s geno...
Article
Full-text available
In livestock social interactions, social genetic effects (SGE) represent associations between phenotype of one individual and genotype of another. Such associations occur when the trait of interest is affected by transmissible phenotypes of social partners. The aim of this study was to estimate SGE and direct genetic effects (DGE, genetic effects o...
Article
The microbiome plays a key role in homeostasis and health and it has been also linked to fertility and semen quality in several animal species including swine. Despite the more than likely importance of sperm bacteria on the boar's reproductive ability and the dissemination of pathogens and antimicrobial resistance genes, the high throughput charac...
Article
Limousin, a renowned beef breed originating from central France, has been selectively bred over the last 100 years to improve economically important traits. We used whole‐genome sequencing data from 10 unrelated Limousin bull calves to detect polymorphisms and identify regions under selection. A total of 13 943 766 variants were identified. Moreove...
Preprint
Full-text available
Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the...
Preprint
Full-text available
Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the...
Preprint
Full-text available
Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the...
Preprint
Full-text available
Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the leve...
Preprint
Full-text available
Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the...
Article
Full-text available
Background The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene r...
Article
Full-text available
We simultaneously measured the fecal microbiota and multiple environmental and host-related variables in a cohort of 185 healthy horses reared in similar conditions during a period of eight months. The pattern of rare bacteria varied from host to host and was largely different between two time points. Among a suite of variables examined, equitation...
Article
Full-text available
Background The pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, little is known about the diversity, host-genetic control, and contributions to host performance of the gut eukaryotic counterparts...
Preprint
Full-text available
Background: Genetic pressure in animal breeding is sparking the interest to select for elite boars with higher sperm quality to maximize ejaculate doses and fertility rates. However, the molecular basis of sperm quality remains largely unexplored. In this study, we sought to identify candidate genes, pathways and DNA variants associated to sperm qu...
Preprint
Full-text available
The microbiome plays a key role in homeostasis and health and it has been also linked to fertility and semen quality in several animal species including swine. Despite the more than likely importance of sperm bacteria on the boar’s reproductive ability and the dissemination of pathogens and antimicrobial resistance genes, a high throughput characte...
Presentation
Full-text available
Bioinformatic pipelines comparison to find the optimal for 16S rRNA gene sequences processing based on its capacity to classify samples according to management and to predict rabbit growth performances.
Preprint
Full-text available
This study aims to characterize commensal fungi and protists inhabiting the gut of healthy pigs, and explore the putative host genetic control over diversity and composition of pig gut eukaryotes. Fecal fungi and protists communities from 514 Duroc pigs of two sexes and two different ages were characterized by 18S and ITS ribosomal RNA gene sequenc...
Article
Full-text available
Background The role of non-coding RNAs in the porcine muscle metabolism is poorly understood, with few studies investigating their expression patterns in response to nutrient supply. Therefore, we aimed to investigate the changes in microRNAs (miRNAs), long intergenic non-coding RNAs (lincRNAs) and mRNAs muscle expression before and after food inta...
Article
Full-text available
Abstract Background Milk quality in dairy cattle is routinely assessed via analysis of mid-infrared (MIR) spectra; this approach can also be used to predict the milk’s cheese-making properties (CMP) and composition. When this method of high-throughput phenotyping is combined with efficient imputations of whole-genome sequence data from cows’ genoty...
Article
Les aptitudes du lait à la transformation en fromage sont étroitement liées à sa composition. Ces caractères, difficiles à mesurer directement, ont été prédits à partir des spectres dans le moyen infrarouge (MIR) du lait en race Montbéliarde (projet From’MIR). Cet article rassemble les résultats de l’analyse du déterminisme génétique des aptitudes...
Article
Full-text available
Motivation: We present Link-HD, an approach to integrate multiple datasets. Link-HD is a generalization of STATIS-ACT ('Structuration des Tableaux A Trois Indices de la Statistique -Analyse Conjointe de Tableaux'), a family of methods designed to integrate information from heterogeneous data. Here, we extend the classical approach to deal with bro...
Article
Full-text available
Muscle development and lipid accumulation in muscle critically affect meat quality of livestock. However, the genetic factors underlying myofiber-type specification and intramuscular fat (IMF) accumulation remain to be elucidated. Using two independent intercrosses between Western commercial breeds and Korean native pigs (KNPs) and a joint linkage-...
Article
Full-text available
In this study we investigated the impact of dietary protein and carotene levels on microbial functions and composition during the last month of purebred fattening Duroc pigs. Fecal microbiota was characterized using 16S ribosomal RNA sequencing at two points of live, 165 (T1) and 195 (T2) days. From 70 to 165 days of age, 32 pigs were divided into...
Article
Full-text available
Background: Feed efficiency (FE) has a major impact on the economic sustainability of pig production. We used a systems-based approach that integrates single nucleotide polymorphism (SNP) co-association and gene-expression data to identify candidate genes, biological pathways, and potential predictors of FE in a Duroc pig population. Results: We...
Article
Full-text available
Mitigation of greenhouse gas emissions is relevant for reducing the environmental impact of ruminant production. In this study, the rumen microbiome from Holstein cows was characterized through a combination of 16S rRNA gene and shotgun metagenomic sequencing. Methane production (CH4) and dry matter intake (DMI) were individually measured over 4–6...
Poster
In this study, an integrative approach with DNA variants, mRNA and lipid related traits were used to identify transcription factors and candidate genes related to lipid metabolism.
Poster
Full-text available
Background The role of non-coding RNAs in the porcine metabolism is poorly understood, with few studies investigating their expression patterns in response to nutrient supply. Therefore, we aimed to investigate the changes of microRNAs (miRNAs), long intergenic non- coding RNAs (lincRNAs) and mRNAs expression before and after food intake. Results...
Poster
In this study, we used whole-genome sequence data to estimate the genetic diversity, structure and putative ancestral origin of the ‘Charolais de Cuba’ (CHCU) breed as well as to identify regions with selective sweeps that may have had an important role in the adaptation to tropical conditions. A total of 12 CHCU samples and 49 samples from 5 breed...