Aboshady, H. M., A. Choury, L. Montout, Y. Félicité, X. Godard, and J. - C. Bambou, "Metagenome reveals caprine abomasal microbiota diversity at early and late stages of Haemonchus contortus infection.", Scientific reports, vol. 13, issue 1, pp. 2450, 2023. Abstract

Haemonchus contortus is one of the most detrimental gastrointestinal nematode parasites for small ruminants, especially in tropics and subtropics. Gastrointestinal nematode and microbiota share the same microhabitat; thus they interact with each other and their host. Metagenomics tools provide a promising way to examine the alterations in the gastric microbial composition induces by gastrointestinal parasites. In this study, we used metagenomics tools to characterize the impact of H. contortus infection on the caprine abomasal microbiota at early and late stage of infection and compared it with non-infected control. Our results showed that H. contortus infection caused a significant increase in abomasal pH at early (7 days post-infection) and late stage of infection (56 days post-infection). The analysis of alpha and beta diversity showed that the microbiota diversity both in number and in proportion was significantly affected at early and late stage of infection. All microbiota classes are impacted by H. contortus infection but Clostridia and Bacteroidia are more concerned. In infected animals, the genera Prevotella decreased at 7 and 56 days post-infection. Here we showed that the abomasal microbiota was significantly affected early after H. contortus infection, and these changes persist at late stage of the infection.

Aboshady, H. M., Y. Félicité, J. Hira, C. Barbier, and J. - C. Bambou, "Early Transcriptome Differences Between Pre-Infected and Naïve Kid Goats Infected With .", Frontiers in veterinary science, vol. 9, pp. 873467, 2022. Abstract

In small ruminant production, gastrointestinal nematode (GIN) infection is one of the major causes of economic losses. The aim of this study was to compare the abomasal mucosa transcriptome of naïve and pre-infected goats at early time points after infection, in order to identify different pathways and upstream regulators involved in the host immune response. Naïve and pre-infected Creole kids were orally infected with 10,000 infective larvae (L3), and abomasal mucosa was sampled at 0, 4, and 6 days post-infection (dpi). At 6 dpi, all the animals were slaughtered to perform parasite burden counts. The mean number of L4 recovered in naïve kids was more than twice as high as that recovered in the pre-infected ones (5,860 and 2,474 respectively, < 0.001). RNA-seq analysis showed a number of differentially expressed genes (DEGs) very low for both naïve and pre-infected animals when comparing day 0 vs. day 4 post-infection. A total of 2,237 and 3,206 DEGs were identified comparing 0 vs. 6 dpi in naïve and pre-infected animals, respectively. Interestingly, only 18 DEGs were found for the comparison of pre-infected vs. naïve animals at 6 dpi. Ingenuity pathway analysis (IPA) showed that several immune responses were activated in pre-infected compared with naïve animals at 0 and 4 dpi such as Th2 and Th1 pathways, natural killer cell, B cell receptor, IL-2, and IL-15 signaling. On the other hand, both naïve and pre-infected animals showed activation for those pathways comparing 6 vs. 0 dpi, with no difference between them. A similar pattern was recorded for upstream regulator genes which were related to immunity like TNF, IL-1β, IL-2, IL-5, TGFβ1, IFNγ, TCR, IL-18, IL-6, and IL-4. Our results showed that at 0 and 4 dpi the immune response was activated toward Th1 and Th2 pathways in pre-infected kids compared to the naïve ones, however, the same immune response was developed in naïve kids as earlier as 6 dpi. We conclude that repeated infection in kid goats induced a concomitant early activation of a Th1 and Th2 immune response resulting in the regulation of worm establishment.

Aboshady, H. M., N. Mandonnet, A. M. Johansson, E. Jonas, and J. - C. Bambou, "Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection.", PloS one, vol. 16, issue 3, pp. e0248405, 2021. Abstract

Gastrointestinal nematodes (GIN) are an important constraint in small ruminant production. Genetic selection for resistant animals is a potential sustainable control strategy. Advances in molecular genetics have led to the identification of several molecular genetic markers associated with genes affecting economic relevant traits. In this study, the variants in the genome of Creole goats resistant or susceptible to GIN were discovered from RNA-sequencing. We identified SNPs, insertions and deletions that distinguish the two genotypes, resistant and susceptible and we characterized these variants through functional analysis. The T cell receptor signalling pathway was one of the top significant pathways that distinguish the resistant from the susceptible genotype with 78% of the genes involved in this pathway showing genomic variants. These genomic variants are expected to provide useful resources especially for molecular breeding for GIN resistance in goats.

Aboshady, H. M., N. Mandonnet, Y. Félicité, J. Hira, A. Fourcot, C. Barbier, A. M. Johansson, E. Jonas, and J. - C. Bambou, "Dynamic transcriptomic changes of goat abomasal mucosa in response to Haemonchus contortus infection.", Veterinary research, vol. 51, issue 1, pp. 44, 2020. Abstract

Gastrointestinal nematode (GIN) infections are one of the major constraints for grazing sheep and goat production worldwide. Genetic selection for resistant animals is a promising control strategy. Whole-transcriptome analysis via RNA-sequencing (RNA-seq) provides knowledge of the mechanisms responsible for complex traits such as resistance to GIN infections. In this study, we used RNA-seq to monitor the dynamics of the response of the abomasal mucosa of Creole goat kids infected with Haemonchus contortus by comparing resistant and susceptible genotypes. A total of 8 cannulated kids, 4 susceptible and 4 resistant to GIN, were infected twice with 10 000 L3 H. contortus. During the second infection, abomasal mucosal biopsies were collected at 0, 8, 15 and 35 days post-infection (dpi) from all kids for RNA-seq analysis. The resistant animals showed early activation of biological processes related to the immune response. The top 20 canonical pathways of differentially expressed genes for different comparison showed activation of the immune response through many relevant pathways including the Th1 response. Interestingly, our results showed a simultaneous time series activation of Th2 related genes in resistant compared to susceptible kids.

Aboshady, H. M., M. J. Stear, A. Johansson, E. Jonas, and J. C. Bambou, "Immunoglobulins as Biomarkers for Gastrointestinal Nematodes Resistance in Small Ruminants: A systematic review.", Scientific reports, vol. 10, issue 1, pp. 7765, 2020. Abstract

The rise of anthelmintic resistance worldwide has led to the development of alternative control strategies for gastrointestinal nematodes (GIN) infections, which are one of the main constraints on the health of grazing small ruminants. Presently, breeding schemes rely mainly on fecal egg count (FEC) measurements on infected animals which are time-consuming and requires expertise in parasitology. Identifying and understanding the role of immunoglobulins in the mechanisms of resistance could provide a more efficient and sustainable method of identifying nematode-resistant animals for selection. In this study we review the findings on immunoglobulin response to GIN in the literature published to date (june 2019) and discuss the potential to use immunoglobulins as biomarkers. The literature review revealed 41 studies which measured at least one immunoglobulin: 35 focused on lamb immune response (18 used non-naïve lambs) and 7 on yearlings. In this review we propose a conceptual model summarizing the role of immunoglobulins in resistance to GIN. We highlight the need for more carefully designed and documented studies to allow comparisons across different populations on the immunoglobulin response to GIN infection.

Aboshady, H. M., N. Mandonnet, M. J. Stear, R. Arquet, M. Bederina, J. Sarry, G. Tosser-Klopp, C. Klopp, A. M. Johansson, E. Jonas, et al., "Transcriptome variation in response to gastrointestinal nematode infection in goats", PLoS ONE , vol. 14, issue 6, pp. e0218719, 2019.
Zidi, A., H. Abo-Shady, A. Molina, A. Menéndez-Buxadera, M. Sánchez-Rodríguez, C. Díaz, M. J. Carabaño, and J. M. Serradilla, "Genome Wide Association for Heat Stress Tolerance/Susceptibility in Florida Dairy Goats", 10th World Congress on Genetics Applied to Livestock Production, Vancouver, Canada, 2014. Abstract

Increasing global temperatures might affect negatively the availability of food resources. Therefore, selecting animals adapted to climate change could be a way to guarantee the continuous production of food. With this motivation, genome wide association analysis (GWAS) for susceptibility/tolerance to heat stress was carried out in Spanish Florida dairy goats (n = 538). Several significant SNPs at whole genome level, located in different chromosomes, were identified. Gene annotation and functional classification analysis carried out with BioMart and DAVID online tools showed significant SNP located in genes involved in milk composition such as kappa casein (CSN3), acetyl-coenzyme A carboxylase alpha (ACACA) and malic enzyme 1 (ME1) and a significant SNP (snp39045-scaffold-3419) mapped at the heat shock 27 kDa associated protein 1 (HSPBAP1) which inhibits the antiapoptotic and thermotolerance function of heat shock protein 27 kDa (HSP27) at cell level

Serradilla, J. M., M. Ramón, H. M. Abo-Shady, A. Molina, M. D. Pérez-Guzmán, C. Díaz, and M. J. Carabaño, "Temperature and humidity effects on performance of high and low yielding dairy sheep and goats.", FAO-CIHEAM Network on Sheep and Goats., Montpellier, France., June 16th – 18th, 2015. Abstract

A total of 49918/1176670 test-day records belonging to 8231/177605 lactating goats/ewes were used to study heat stress in Spanish dairy goats (Florida breed) and sheep (Manchega breed). The productive traits investigated were daily milk, fat and protein yield. The tolerance threshold and the slope of the response of these traits to heat stress have been calculated. Test day records from each herd were merged with maximum and average daily temperature and a temperature-humidity index (THI) registered in weather stations the day of milk recording. Two sets of data were analysed: data from high milk yielding animals and data from low milk yielding animals. Two thresholds were found, one for low temperatures and the other for high temperatures. Climatic effects on yields were less marked in the case of ewes. No very important differences were found between high and low productive animals in respect to thresholds and slopes, except for the decay of fat and protein yields due to heat stress.

Abo-Shady, H. M., Genetic response of heat stress on performance of Spanish local dairy goat breed., , Valencia, Spain, Polytechnic University of Valencia, 2013. Abstract

In the present thesis the effect of heat stress on milk, fat, and protein yields and fat and protein contents has been studied in the Spanish Florida breed of dairy goats. It comprises three chapters: The first one is a bibliographic review of the state of the art. The second one is a phenotypic analysis carried out to determine the climatic variables most correlated to the production traits and to estimate the tolerance thresholds and slopes of the responses of the dairy traits studied to heat stress. The third chapter is a genetic analysis of formerly cited responses, undertaken with the objective to estimate the environmental and genetic (co)variance components of heat stress tolerance. A total of 185,675 test-day records belonging to 13,481 lactating goats distributed in 20 flocks, collected between 2006 and 2012, combined with maximum and average temperatures and the values of an index of temperature and relative humidity (THI), registered the day of milk recording and one and two days before in meteorological stations located less than 22 Km from the farms, were used for the phenotypic and genetic analysis. For the first study, a Ridge regression analysis and a GLM select analysis were carried out in order to select the climatic variables and dates that were recorded, having the highest correlations with the dairy traits under study. Then, tolerance thresholds and slopes of the regressions of these traits with the selected climatic variables were estimated with spline and polynomial models by means of Bayesian methods. Results shows that the maximum and average temperatures (mean of maximum and minimum temperatures) explain the change in dairy traits caused by climatic effects better than the THI. Temperatures registered the day of milk recording or one day before have more effect on the traits studied than those registered two days before. Generally, yields and contents of milk components decrease when temperature increases. However, milk yield seem to be less affected by high temperatures, being more affected by cold temperatures. Climatic variables have a higher effect on milk composition in high productive animals in respect to the rest. For the genetic analysis, a reaction norm animal model (RNM) was used to estimate the genetic and permanent environmental (co)variance components of the relation of dairy traits with THI, maximum and average temperature, modeling this relation by means of Legendre polynomials. Results show that the heritability of dairy traits tends to decrease for increasing values of the climatic variables. Genetic correlations between the intercept and the slope of each model, and between the first and the subsequent points in the scales of the climatic variables, provide evidences that selection for better milk performance will reduce heat stress tolerance. The genetic variation of the response to heat stress found in this analyses could be used to select animals according to their response to heat stress (robust, tolerant and non-tolerant).

Abo-Shady, H. M., Sexual behaviour and reproductive performance of Zaraibi and Damascus does as affected by different senses., : M.SC. Thesis, Fac. Agric., Cairo Univ., Egypt, 2012. Abstract

Twenty three Zaraibi and sixteen Damascus does were used to investigate the influence of tactile, olfactory and auditory stimuli of bucks on sexual behavior and LH secretion. Does of each breed were randomly allotted into four groups. Does of the first group served as a control. In the second group, does were joined by an intact male of the same breed (tactile group). Does of the third group were exposed to buck hair (olfactory group). The fourth group was subjected to recorded buck voice (auditory group). Tests were carried out for 30 min. twice a day for three days. Behavioral displays of does were recorded for each doe in the four groups. Blood samples were collected immediately before treatment then every 12 hour for 72 hours to assay LH and estradiol concentrations. Does of both breeds responded significantly to the different stimuli. Tactile and olfactory stimuli resulted in estrus of 67% and 50% of Zaraibi and Damascus does, respectively. Relatively lower response due to vocalization was observed in Zaraibi and Damascus does (50% and 25%, respectively). Response to vocalization in Damascus does was not significantly different from that of the non-stimulated (control) group. Reaction time in both breeds was similar and generally ranged from 36 to 60 h regarding behavioral displays. Results showed no significant differences due to breed or stimulus in search for male or urination. Meanwhile, vocalization percentage, tailing, degree of isolation and degree of restlessness displays were significantly (P<0.05) affected between groups tested. No vaginal changes (edema of the vulva and mucous discharge) were observed in both breeds in response to any stimulus. The only exception was that 33% of Zaraibi does (2/6) responded to tactile stimulus. Results showed that Zaraibi does subjected to buck hair had the highest LH concentration at 36 h and at 72 h after treatment (0.75 IU/L) compared with other treatments as well as Damascus breed. The highest concentration of LH was that of Zaraibi does exposed to buck voice at 48 h after treatment (0.87 IU/L). Exposure of Zaraibi does to buck’s odour and voice may induce sexual behavior and ovulation within 1.5 – 3 days.