Yuliaxis Ramayo-Caldas

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

[This corrects the article DOI: 10.1371/journal.pone.0284481.].

C-reactive protein (CRP) is an evolutionary highly conserved protein. Like humans, CRP acts as a major acute phase protein in pigs. While CRP regulatory mechanisms have been extensively studied in humans, little is known about the molecular mechanisms that control pig CRP gene expression. The main goal of the present work was to study the regulator...

Microbiome-host interactions have profound effects on metabolic functions and physiological processes that influence growth, production efficiency, animal welfare and the robustness of the ruminant holobiont. Interactions between the host and its microbiome are influenced by both external and host-specific factors. While the influence of the extern...

Background Most interactions between the host and its microbiota occur at the gut barrier, and primary colonizers are essential in the gut barrier maturation in the early life. The mother–offspring transmission of microorganisms is the most important factor influencing microbial colonization in mammals, and C-section delivery (CSD) is an important...

Genetic variation in the pig genome partially modulates the composition of porcine gut microbial communities. Previous studies have been focused on the association between single nucleotide polymorphisms (SNPs) and the gut microbiota, but little is known about the relationship between structural variants and fecal microbial traits. The main goal of...

Background Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction of complex traits, although methods to optimize this are still largely unexplored. In this paper, we assess the impact of different modelling str...

Mixing, a common management strategy used to regroup pigs, has been reported to impair individual performance and affect pig welfare because of the establishment of a new social hierarchy after regrouping. In this study we aimed to determine whether mixing management (non-mixed vs. mixed) and gender (gilts vs. barrows) affect the social and non-soc...

Pig industry is facing new challenges that make necessary to reorient breeding programs to produce more robust and resilient pig populations. The aim of the present work was to study the genetic determinism of lymphocyte subpopulations in the peripheral blood of pigs and identify genomic regions and biomarkers associated to them. For this purpose,...

A better understanding of the environmental and host factors modulating gut microbiomes is a topic of greatest interest. Recent evidence suggests that host genetic diversity loss constraints gut microbial ecosystems' heterogeneity. However, host genetics and gut microbiota diversity are typically studied independently. Here we propose to rethink di...

In recent years, an increased number of studies have dealt with the analysis of social dominance related to animal behavior, physiology, and performance. This study aimed to investigate whether hierarchical ranking affects the coping style, non-social behavior during open field and novel object tests, performance, and physiological parameters of pi...

Fatty acids (FAs) play an essential role as mediators of cell signaling and signal transduction, affecting metabolic homeostasis and determining meat quality in pigs. However, FAs are transformed by the action of several genes, such as those encoding desaturases and elongases of FAs in lipogenic tissues. The aim of the current work was to identify...

Background: In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, a...

Background The effect of the cecal microbiome on growth of rabbits that were fed under different regimes has been studied previously. However, the term “effect” carries a causal meaning that can be confounded because of potential genetic associations between the microbiome and production traits. Structural equation models (SEM) can help disentangle...

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....

Background Genetic variation in the pig genome partially modulates the composition of porcine gut microbial communities. Previous studies have been focused on the association between single nucleotide polymorphisms (SNPs) and the gut microbiota, but little is known about the relationship between structural variants and gut microbial traits. Result...

Background The mother-newborn transmission of microorganisms is the most important factor influencing microbial colonization in the neonate, and C-section delivery (CSD) is an important disruptive factor of this transfer. Although this medical procedure saves countless lives, it may also have costs. Recently, the deregulation of symbiotic host-micr...

Fatty acids (FAs) play an essential role as mediators of cell signaling and signal transduction, affecting metabolic homeostasis and determining meat quality in pigs. However, FAs are transformed by the action of several genes, as those encoding desaturases and elongases of FAs in lipogenic tissues. The aim of the current work was to identify candi...

The contribution of microRNAs (miRNAs) to mRNA post‐transcriptional regulation has often been explored by the post hoc selection of downregulated genes and determining whether they harbor binding sites for miRNAs of interest. This approach, however, does not discriminate whether these mRNAs are also downregulated at the transcriptional level. Here,...

Modulating early-life microbial colonization through xylo-oligosacharides (XOS) supplementation represents an opportunity to accelerate the establishment of fiber-degrading microbial populations and improve intestinal health. Ninety piglets from 15 litters were orally administered once a day from d7 to d27 of lactation with either 5 mL of water (CO...

Background: Reducing enteric methane emissions from farmed ruminants can be achieved by various nutritional strategies. However, it remains unclear to what extent the effects of diet on rumen microbiome are comparable between different ruminant species. In this work, we compared the effects of starch- and/or lipids-rich diets on the rumen microbiom...

The objective of this work was to assess the ability of holobiont data (i.e., host’s genotype and microbiota) to predict six immunity traits in 400 pigs. We propose the term ‘predictome’ to mean a systematic study of as many predictive methods as possible. With this spirit, we compare REML, Bayes C, and Bayesian reproducing kernel Hilbert space (RK...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

Background: Feed efficiency is a paramount concept for the environmental and economical sustainability of rabbit production. In this sense, identifying all the components involved in its determinism is highly desirable. Microbial communities inhabiting the intestinal tract play an important role in nutrient absorption and could also impact rabbit g...

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...

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...

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...

Abstract 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 ev...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...