Moawad, M. A., H. M. Aboshady, M. S. Abd-Alla, N. Ghanem, A. Y. Abdel-Moneim, M. Nishibori, T. Yonezawa, H. Mannen, and R. Agamy, "Genetic polymorphisms of the Growth Hormone (GH) gene in Damascus and Black Bengal male goats.", Tropical animal health and production, vol. 57, issue 1, pp. 18, 2025. Abstract

Sustainable agriculture approaches necessitate a concerted effort from researchers to establish paths that meet global population needs without compromising environmental resources. Goats are unique among ruminants because of their ability to adapt to some of the harshest environments around the world. Growth Hormone (GH) gene is a major regulator of muscle mass growth. Therefore, our study aims to analyze the whole sequence of GH gene in order to identify various single nucleotide polymorphisms (SNPs) in Damascus and Black Bengal goats (BBG) and to predict the effect of mutant residues on the protein's structure and function. Additionally, this study examined the effects of these SNPs on growth characteristics in Damascus goats. The study was designed to test 22 male goats. To obtain high-quality amplification of the GH gene, we utilized the nested PCR technique and performed paired-end sequencing for each fragment. Sequences alignment in the GH gene of Damascus and BBG goats unveiled 25 SNPs with different frequencies within the two breeds. Seven SNPs identified in coding regions comprised four synonymous variants (719 C → T, 731 G → A, 1610 C → T and 1625 C → T) and three non-synonymous variants (1112 G → A, 1459 C → T and 1470 C → T). The SNP 1112 G → A led to the substitution of Glutamic acid with Lysine (E/K) at amino acid position 137. The SNP 1459 C → T led to the substitution of Alanine with Valine (A/V) at amino acid position 160. Meanwhile, the SNP 1470 C → T led to the substitution of Leucine with Phenylalanine(L/F) at amino acid position 164. The SNP 1112 G → A was predicted to have a deleterious effect on the protein's structure and function. The SNPs 914 G → A and 1112 G → A showed significant differences (P < 0.05) between genotypes in pre-slaughter weight and almost carcass cuts in Damascus goats, indicating their possible use in breeding programs as a potential genetic marker for weight/size in goats as well as in assessing and choosing members of this breed for meat production.

Rashid, M., H. M. Aboshady, R. Agamy, and H. Archimede, "Milk production and composition in warm-climate regions: a systematic review and meta-analysis.", Tropical animal health and production, vol. 56, issue 8, pp. 382, 2024. Abstractrashid_et_al._2024_milk_production_tahp.pdf

Milk production is a key component of the agriculture sector in the tropics and subtropics, contributing 47.32% to global milk production. This study aimed to quantify milk production and composition (fat and protein) in warm-climate regions located between 30 degrees north and south of the equator. A meta-analysis was conducted using the standardized mean (SM) for milk production, fat percentage, and protein percentage, all adjusted for dry matter intake (DMI), focusing on lactating ruminants. A total of 42, 11, 15, and 16 research papers were selected for cows, buffalo, sheep, and goats, respectively, encompassing 2421 animal records from experiments published between 1992 and 2024. The SM for milk production was 10.38, 9.77, 0.79, and 1.13 kg/day/animal for cows, buffalo, sheep, and goats, respectively. Due to the significant variance between different cow breeds, the study divided the cows into three main groups based on breed type crossbreds, foreign, and local breeds. The SM for milk production per animal was 11.49 kg/day for crossbreds, 22.95 kg/day for foreign breeds, and 7.13 kg/day for local breeds. The effect of DMI on the SM of milk production for cows, sheep, and goats was highly significant. For milk fat, the SM was 3.95, 6.64, 4.70, and 3.56% for cows, buffalo, sheep, and goats, respectively. Regarding milk protein, the SM was 3.36, 3.91, 4.34, and 3.45% for cows, buffalo, sheep, and goats, respectively. The results of this meta-analysis highlight that warm-climate regions are significant contributors to global dairy production. Furthermore, improving ruminant milk production and quality in hot climates need further efforts.

Moawad, M. A., H. M. Aboshady, R. Agamy, N. Ghanem, A. Y. Abdel-Moneim, and M. A. - A. S. 1, "Using Body Measurements and Real-Time Ultrasound to Evaluate Carcass Characteristics of Male Damascus Kids", Egyptian Journal of Veterinary Sciences, pp. 1-17, 2024. Abstract

Linear body measurements and real-time ultrasound may serve as crucial factors in cost-effective carcass prediction, thereby facilitating value-based marketing of living animals. The current study aimed to evaluate carcass components and cuts of male Damascus kids from body and ultrasound measurements. Besides investigate the effect of presence of horns and type of birth (single or twins) on body measurements and carcass characteristics. Thirteen male Damascus kids aged 12 months were used in the study. Ultrasound measurements were taken with probe (7.5 MHZ) between the 12th and 13th thoracic vertebra on live kids.
Body measurements, carcass components and cuts of horned kids were higher than those of hornless ones. The birth type showed no significant influence on body weight and measurements at 12 months and on carcass components and cuts. Body length was entered in all prediction equations to predict carcass cuts and measurements. Afterward, heart girth and chest width were the most variables used in prediction equations. Ultrasound measurements (depth, area, width) of rib-eye muscle on live kids led to accurate prediction for weights of hot carcass, leg, flank, shoulder, neck, best end of neck, middle neck in their carcasses. Accurate prediction equations were obtained to predict real eye muscle width, depth and area using ultrasound measurements of rib-eye muscle width, depth, area, respectively. R2 accounted 33% to predict width of rib-eye muscle (P<0.05). Moreover, ultrasound depth and area of rib-eye muscle contributed 51% and 61%, respectively of the total variation in real depth and area of eye muscle (P<0.01).

Aboshady, H. M., E. Jorge-Smeding, S. Taussat, and G. Cantalapiedra-Hijar, "Development and validation of a model for early prediction of residual feed intake in beef cattle using plasma biomarkers.", Animal : an international journal of animal bioscience, vol. 18, issue 11, pp. 101354, 2024. Abstract

Identification of plasma biomarkers for feed efficiency in growing beef cattle offers a promising opportunity for developing prediction models to improve precision feeding strategies. However, these models must accurately predict feed efficiency at early stages of fattening. Our study aimed to evaluate the reliability of candidate biomarkers previously identified in late-fattening cattle when analysed during early fattening stages and to develop diet-specific prediction equations for residual feed intake (RFI). From a total of 364 Charolais bulls across seven cohorts, we selected 64 animals with extreme RFI values. The animals were fed either a corn‑ or grass-silage diets. These animals were chosen from four out of the available seven cohorts. Animals from three cohorts (24 high-RFI and 24 low-RFI, having a mean RFI difference of 1.48 kg/d) were used for biomarker confirmation and prediction model training. Animals from a fourth cohort (8 high-RFI and 8 low-RFI, having a mean RFI difference of 0.98 kg/d) were used for model external validation. Blood samples were collected at the beginning of the feed efficiency test (333 ± 20 days), and plasma underwent targeted metabolomic for 630 metabolites, natural abundance of N (δN), insulin, and IGF-1 analysis. Seven previously identified plasma biomarkers for RFI in late-fattening beef cattle still kept their capability for discriminating low and high RFI animals when analysed during early fattening stages (P < 0.05). Among these confirmed biomarkers, five were common for both grass- and corn-fed animals (creatinine, β-alanine, triglyceride TG18:0_34:2, symmetric dimethyl-arginine and phosphatidylcholine PC aa C30:2) while two were diet-specific (IGF-1 for grass silage-based diet, and isoleucine for corn silage-based diet. No new plasma biomarkers of RFI were identified at early-fattening stages (false discovery rate  > 0.05). Prediction models were developed based on seven confirmed RFI biomarkers analysed during early-fattening. Two logistic regression models incorporating creatinine and either IGF-1 (for grass silage-based diet) or PC aa C30:2 (for corn silage-based diet) effectively distinguished between high- and low-RFI animals with high sensitivity and specificity (area under the curve > 0.80). The biomarkers used in the models showed moderate to high repeatability between early and late fattening stages (0.45 < r < 0.65). The models were successfully externally validated, with more than 85% of animals from the fourth cohort correctly classified. Once validated in larger cohorts and utilising cost-effective and rapid analytical methods, these models could support precision feeding and breeding programmes, aiming to reduce the cost of raising beef cattle.

Aboshady, H. M., A. Gavriilidou, N. Ghanem, M. A. Radwan, A. Elnahas, R. Agamy, N. H. Fahim, M. H. Elsawy, A. - M. B. M. Shaarawy, A. M. Abdel-Hafeez, et al., "Gut Microbiota Diversity of Local Egyptian Cattle Managed in Different Ecosystems.", Animals : an open access journal from MDPI, vol. 14, issue 18, 2024. Abstract

The animal gastrointestinal tract contains a complex microbiome whose composition ultimately reflects the co-evolution of microorganisms with their animal host and their host's environment. This study aimed to gain insights into the adaptation of the microbiota of local Egyptian cattle to three different ecosystems (Upper Egypt, Middle Egypt, and Lower Egypt) distributed across 11 governorates (with an average of 12 animals per governorate) using amplicon sequencing. We analyzed the microbiota from 136 fecal samples of local Egyptian cattle through a 16S rRNA gene sequencing approach to better understand the fecal microbial diversity of this breed which developed under different ecosystems. An alpha diversity analysis showed that the fecal microbiota of the Egyptian cattle was not significantly diverse across areas, seasons, sexes, or farm types. Meanwhile, microbiota data revealed significant differences in richness among age groups ( = 0.0018). The microbial community differed significantly in the distribution of its relative abundance rather than in richness across different ecosystems. The taxonomic analysis of the reads identified and as the dominant phyla, accounting for over 93% of the total bacterial community in Egyptian cattle. Middle Egypt exhibited a different microbial community composition compared to Upper and Lower Egypt, with a significantly higher abundance of and and a lower abundance of in this region than the other two ecosystems. Additionally, Middle Egypt had a significantly higher relative abundance of the family and the genera than Lower and Upper Egypt. These results suggest a difference in the adaptation of the fecal microbial communities of Egyptian cattle raised in Middle Egypt. At the genus level, eleven genera were significantly different among the three ecosystems including , , , , , , , , , , and . These significant differences in microbiota composition may impact the animal's adaptation to varied environments.

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.

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