Additional file 3: Table S2. of Novel equine tissue miRNAs and breed-related miRNA expressed in serum

Known and novel miRNAs expression values. An Excel table with normalized count per million values (cpm) for each of the known and novel miRNAs expressed at > 1 cpm in 90 % of samples. (XLSX 519 kb

Ingredient and chemical composition of the diets.

<p>Ingredient and chemical composition of the diets.</p

Regulatory network of transcription factors, miRNAs and target genes using Cytoscape.

<p>Schematic visualization of shared associations between transcription factors (TFs), miRNAs, and differentially expressed genes when comparing Nutr with Conv. The network is displayed graphically as nodes (genes, TFs, and miRNAs) and edges (the biological relationship between nodes). Node color intensity indicates the expression of the association: red = upregulation with Nutr diet, green = downregulation with Nutr diet. Node shape indicates whether it is a TF (triangle) or an miRNA (round) or other kinds of molecule.</p

Heatmap of correlations between gene expression changes and phenotypic variations. Correlations were estimated for growth performances and carcass traits (A), liver weight, pH, and chemical composition (B), and liver fatty acid composition (groups of fatty acids) (C).

<p>The heatmap was generated using the CorrPlot package in R. The gene was included in the heatmap when a significant correlations for at least one phenotype was found (<i>P</i> < 0.05, Pearson product-moment correlations). Blue indicates negative correlations with values <i>r</i> < -0.51; grey indicates correlations values in the range -0.50 < <i>r</i> < 0.50; red color indicates positive correlations with <i>r</i> values > 0.51. BW: body weight; DG: daily gain; FS_IV: fat covering <i>in vivo</i>; MS_IV: body conformation; CW: carcass weight; MS_PM: carcass muscularity score; FS_PM: carcass fatness score; WT: liver weight. DM: dry matter; SFA: saturated fatty acids; MUFA: monounsaturated fatty acids; PUFA: polyunsaturated fatty acids; SCFA: fatty acids < C16; C16: fatty acids with 16 carbon chains; LCFA: fatty acids > C16; OCFA: odd-chain fatty acids; BCFA: branched-chain fatty acids; TFAC18_mono: Trans C18:1 fatty acids; CLAct_tc: conjugated linoleic acid <i>c</i>,<i>t/t</i>,<i>c</i> isomers; n_Ratio: ratio n-6/n-3.</p

Liver fatty acid (FA) contents¹ of young bulls fed conventional (Conv), low-impact (LowI) and nutraceutical (Nutr) diets.

<p>Liver fatty acid (FA) contents<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167747#t002fn003" target="_blank">¹</a> of young bulls fed conventional (Conv), low-impact (LowI) and nutraceutical (Nutr) diets.</p

Multidimensional scaling (MDS) analysis using log2 of all normalized unique gene counts (n = 24,596).

<p>Conv: conventional diet; LowI: low-impact diet; Nutr: nutraceutical diet.</p

Significant differences in splicing events among the three diet groups (conventional, low-impact and nutraceutical).

<p>Significant differences in splicing events among the three diet groups (conventional, low-impact and nutraceutical).</p

Ingredient and chemical composition of the diets.

<p>Ingredient and chemical composition of the diets.</p

Table4.XLS

<p>Gastrointestinal strongyles are a major threat to horses' health and welfare. Given that strongyles inhabit the same niche as the gut microbiota, they may interact with each other. These beneficial or detrimental interactions are unknown in horses and could partly explain contrasted susceptibility to infection between individuals. To address these questions, an experimental pasture trial with 20 worm-free female Welsh ponies (10 susceptible (S) and 10 resistant (R) to parasite infection) was implemented for 5 months. Fecal egg counts (FEC), hematological and biochemical data, body weight and gut microbiological composition were studied in each individual after 0, 24, 43, 92 and 132 grazing days. R and S ponies displayed divergent immunological profiles and slight differences in microbiological composition under worm-free conditions. After exposure to natural infection, the predicted R ponies exhibited lower FEC after 92 and 132 grazing days, and maintained higher levels of circulating monocytes and eosinophils, while lymphocytosis persisted in S ponies. Although the overall gut microbiota diversity and structure remained similar during the parasite infection between the two groups, S ponies exhibited a reduction of bacteria such as Ruminococcus, Clostridium XIVa and members of the Lachnospiraceae family, which may have promoted a disruption of mucosal homeostasis at day 92. In line with this hypothesis, an increase in pathobionts such as Pseudomonas and Campylobacter together with changes in several predicted immunological pathways, including pathogen sensing, lipid metabolism, and activation of signal transduction that are critical for the regulation of immune system and energy homeostasis were observed in S relative to R ponies. Moreover, S ponies displayed an increase in protozoan concentrations at day 92, suggesting that strongyles and protozoa may contribute to each other's success in the equine intestines. It could also be that S individuals favor the increase of these carbohydrate-degrading microorganisms to enhance the supply of nutrients needed to fight strongyle infection. Overall, this study provides a foundation to better understand the mechanisms that underpin the relationship between equines and natural strongyle infection. The profiling of horse immune response and gut microbiota should contribute to the development of novel biomarkers for strongyle infection.</p

Image8.TIF

<p>Gastrointestinal strongyles are a major threat to horses' health and welfare. Given that strongyles inhabit the same niche as the gut microbiota, they may interact with each other. These beneficial or detrimental interactions are unknown in horses and could partly explain contrasted susceptibility to infection between individuals. To address these questions, an experimental pasture trial with 20 worm-free female Welsh ponies (10 susceptible (S) and 10 resistant (R) to parasite infection) was implemented for 5 months. Fecal egg counts (FEC), hematological and biochemical data, body weight and gut microbiological composition were studied in each individual after 0, 24, 43, 92 and 132 grazing days. R and S ponies displayed divergent immunological profiles and slight differences in microbiological composition under worm-free conditions. After exposure to natural infection, the predicted R ponies exhibited lower FEC after 92 and 132 grazing days, and maintained higher levels of circulating monocytes and eosinophils, while lymphocytosis persisted in S ponies. Although the overall gut microbiota diversity and structure remained similar during the parasite infection between the two groups, S ponies exhibited a reduction of bacteria such as Ruminococcus, Clostridium XIVa and members of the Lachnospiraceae family, which may have promoted a disruption of mucosal homeostasis at day 92. In line with this hypothesis, an increase in pathobionts such as Pseudomonas and Campylobacter together with changes in several predicted immunological pathways, including pathogen sensing, lipid metabolism, and activation of signal transduction that are critical for the regulation of immune system and energy homeostasis were observed in S relative to R ponies. Moreover, S ponies displayed an increase in protozoan concentrations at day 92, suggesting that strongyles and protozoa may contribute to each other's success in the equine intestines. It could also be that S individuals favor the increase of these carbohydrate-degrading microorganisms to enhance the supply of nutrients needed to fight strongyle infection. Overall, this study provides a foundation to better understand the mechanisms that underpin the relationship between equines and natural strongyle infection. The profiling of horse immune response and gut microbiota should contribute to the development of novel biomarkers for strongyle infection.</p