Animals

18 pages, 962 KB

Open AccessArticle

Genetic Parameters for Rumination Time, Daily Average Milk Temperature, and Milking Traits Derived from Automatic Milking Systems in Holstein Cattle

by Ali Altınsoy, Hacer Yavuz Altınsoy, Serdar Duru and İsmail Filya

Animals 2026, 16(3), 362; https://doi.org/10.3390/ani16030362 (registering DOI) - 23 Jan 2026

Abstract

Automatic Milking Systems (AMSs) enable the continuous recording of production, milkability, behavioral, and physiological traits, offering new opportunities for genetic evaluation in dairy cattle. This study aimed to estimate variance components and genetic parameters for milk yield-related traits, milking efficiency traits, rumination time [...] Read more.

Automatic Milking Systems (AMSs) enable the continuous recording of production, milkability, behavioral, and physiological traits, offering new opportunities for genetic evaluation in dairy cattle. This study aimed to estimate variance components and genetic parameters for milk yield-related traits, milking efficiency traits, rumination time (RT), and daily average milk temperature (MTEMP) using AMS-derived data from 1252 Holstein cows. 65,475 weekly records from a single commercial herd were analyzed using repeatability animal models fitted by restricted maximum likelihood. Heritability estimates were moderate to high for milking time (MT) (0.31), milking speed (MS) (0.38), RT (0.30), and MTEMP (0.28), whereas behavioral traits such as number of milking (NoM) (0.26) and number of refused (NoREF) (0.11) showed lower but meaningful heritabilities. Repeatability was highest for MT and MS (0.77 and 0.79), indicating consistent milking performance across repeated records. MTEMP demonstrated clear seasonal variation, increasing in warmer periods and decreasing during colder months, indicating sensitivity to environmental conditions. Genetic correlations among traits revealed both favorable and unfavorable associations; however, several estimates were associated with relatively large standard errors and should therefore be interpreted with caution. The inclusion of MTEMP as a proxy physiological trait derived from AMS data showed measurable genetic variation, although its biological interpretation requires careful consideration. Overall, the results suggest that AMS-derived phenotypes may contribute useful information for genetic studies of functional traits, but the single-herd structure, limited pedigree depth, and data aggregation procedures restrict the generalizability of the findings. Further multi-herd and genomics-based studies are required to validate these results and assess their applicability in breeding programs. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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24 pages, 2811 KB

Open AccessFeature PaperArticle

Autochthonous and Allochthonous Gut Microbes May Work Together: Functional Insights from Farmed Gilthead Sea Bream (Sparus aurata)

by Alvaro Belenguer, Federico Moroni, Fernando Naya-Català, Paul George Holhorea, Ricardo Domingo-Bretón, Josep Àlvar Calduch-Giner and Jaume Pérez-Sánchez

Animals 2026, 16(3), 360; https://doi.org/10.3390/ani16030360 (registering DOI) - 23 Jan 2026

Abstract

In fish gut microbiome studies, there are no standardized protocols regarding sampling region or post-feeding time, nor clear consensus on whether analyses should target resident (autochthonous) or transient (allochthonous) bacteria. This study examined the dynamics and interactions of both microbial communities in the [...] Read more.

In fish gut microbiome studies, there are no standardized protocols regarding sampling region or post-feeding time, nor clear consensus on whether analyses should target resident (autochthonous) or transient (allochthonous) bacteria. This study examined the dynamics and interactions of both microbial communities in the anterior and posterior intestine of farmed gilthead sea bream and evaluated the resident microbiome at 24 and 48 h post-feeding. Microbial DNA was sequenced using the Oxford Nanopore Technology platform. Data were analyzed through statistical and discriminant approaches, as well as a Bayesian network framework to assess bacterial interactions. Transient communities showed higher richness and diversity, regardless of intestinal section, suggesting a more specialized and stable microbial environment in the mucus layer. The two communities differed markedly in structure and composition. Variations associated with intestinal region were less pronounced, particularly for autochthonous bacteria, and post-feeding fluctuations in the resident microbiome were minimal. Functionally, results indicated relevant synergies between communities. Protein metabolism pathways were enriched in autochthonous bacteria, whereas allochthonous microorganisms contributed mainly to bile acid and carbohydrate metabolism. Overall, resident and transient bacteria constitute distinct communities in the gut of gilthead sea bream, with numerous genera present in both but most being differentially represented and interconnected. Full article

(This article belongs to the Special Issue Fish Microbiome, a Novel Tool to Improve Sustainable Production and Welfare in Aquaculture)

21 pages, 2042 KB

Open AccessArticle

Leveraging Fst and Genetic Distance to Optimize Reference Sets for Enhanced Cross-Population Genomic Prediction

by Le Zhou, Lin Zhu, Fengying Ma, Mingjuan Gu, Risu Na and Wenguang Zhang

Animals 2026, 16(3), 359; https://doi.org/10.3390/ani16030359 (registering DOI) - 23 Jan 2026

Abstract

Genomic selection often faces challenges of insufficient prediction accuracy in cross-population applications, primarily due to differences in linkage disequilibrium patterns between populations. This study proposes an Fst-based strategy to enhance prediction performance by constructing a cross-population reference set with high genetic similarity to [...] Read more.

Genomic selection often faces challenges of insufficient prediction accuracy in cross-population applications, primarily due to differences in linkage disequilibrium patterns between populations. This study proposes an Fst-based strategy to enhance prediction performance by constructing a cross-population reference set with high genetic similarity to the target population (PopA). By integrating Fst-mediated SNP screening and Euclidean genetic distance analysis, the top 10%, 15% and 20% of individuals genetically most similar to PopA were screened from PopB and PopC, respectively, leading to the generation of six reference sets characterized by different mixing proportions. The results demonstrate that incorporating the top 10–20% of the most similar individuals significantly improves the accuracy and robustness of genomic estimated breeding value predictions. Among the methods evaluated, ssGBLUP and wGBLUP performed best, with prediction accuracy increasing as the mixing proportion rose up to 20%. This approach effectively mitigates structural bias caused by inter-population genetic differences and significantly enhances prediction efficiency. The multi-level mixing experiment not only validates the practical value of Fst and Euclidean distance but also provides theoretical support and a feasible solution for the efficient integration of cross-population germplasm resources. Full article

(This article belongs to the Collection Advances in Cattle Breeding, Genetics and Genomics)

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15 pages, 2489 KB

Open AccessArticle

Surveillance of Swine Coronaviruses in Hungarian Herds with a Newly Established Pan-Coronavirus RT-PCR System

by Dóra Máté, Renáta Varga-Kugler, Eszter Kaszab, Henrik Fülöp Károlyi, Tamás Görföl, Gábor Kemenesi, Barbara Igriczi, Gyula Balka, Marianna Domán, Ádám Bálint, Zoltán Zádori and Enikő Fehér

Animals 2026, 16(3), 358; https://doi.org/10.3390/ani16030358 (registering DOI) - 23 Jan 2026

Abstract

The rapid evolution of coronaviruses (CoVs) requires researchers to develop specific yet broad-spectrum detection methods to monitor their constant genomic changes. The goal of the present study was to establish a current pan-coronavirus RT-PCR system capable of detecting a wide variety of CoVs [...] Read more.

The rapid evolution of coronaviruses (CoVs) requires researchers to develop specific yet broad-spectrum detection methods to monitor their constant genomic changes. The goal of the present study was to establish a current pan-coronavirus RT-PCR system capable of detecting a wide variety of CoVs and useful for the investigation of virus diversity and host spectrum. For optimization, one-step and two-step nested RT-PCRs with three RT enzymes were examined, amplifying a ~600 bp long product of the RNA-dependent RNA polymerase. As templates, the in vitro transcribed RNA of ten pathogenic CoVs (SARS-CoV, SARS-CoV-2, NL-63, OC43, feline CoV, porcine epidemic diarrhea virus or PEDV, transmissible gastroenteritis virus or TGEV, canine CoV, bat CoV, and infectious bronchitis virus) were applied instead of the often-used DNA standards. A limit of detection of 5–50 copies/reaction was achieved with a random hexamer-primed two-step RT-PCR and a touchdown cycling profile, representing a lower detection limit and higher specificity compared to previously published primer sets. Swine origin pooled samples (n = 121), collected from apparently healthy herds in Hungary, were tested with the novel RT-PCR system. Sequences of porcine respiratory CoV/TGEV and porcine hemagglutinating encephalomyelitis virus were identified in 24 oral fluid and nasal swab pools, demonstrating the circulation of these viruses in this country, as well as the suitability of the new PCR for their detection. The results highlighted the importance of adequate RT enzyme selection and the use of RNase inhibitors in sample preparation and conservation. Full article

(This article belongs to the Section Veterinary Clinical Studies)

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16 pages, 643 KB

Open AccessArticle

Evaluating Adjusted ssGBLUP Models for Genomic Prediction and Matrix Compatibility in South African Holstein Cattle

by Kgaogelo Stimela Mafolo, Michael D. MacNeil, Frederick W. C. Neser and Mahlako Linah Makgahlela

Animals 2026, 16(3), 357; https://doi.org/10.3390/ani16030357 (registering DOI) - 23 Jan 2026

Abstract

In populations with limited genotyping, single-step genomic best linear unbiased predictions (ssGBLUP) can produce biased or less accurate genomic predictions due to incompatibilities between genomic and pedigree relationship matrices. The study evaluated the impact of five alternative ssGBLUP models for genomic predictions of [...] Read more.

In populations with limited genotyping, single-step genomic best linear unbiased predictions (ssGBLUP) can produce biased or less accurate genomic predictions due to incompatibilities between genomic and pedigree relationship matrices. The study evaluated the impact of five alternative ssGBLUP models for genomic predictions of milk, fat, and protein yield production traits in South African Holstein cattle. The dataset included 696,413 milk production records and pedigrees of 541,325 animals. Production traits were 305-day lactation yields for milk, protein, and fat. Genotype data were based on the Illumina 50K chip v3, with 53,218 SNPs. A total of 1221 animals with genotypes and 41,407 SNP markers were in the final dataset. The five models used to estimate genomic estimated breeding values (GEBVs) were the single-step method (ssGBLUP), ssGBLUP accounting for inbreeding (ssGBLUP_Fx), ssGBLUP with unknown parent groups (ssGBLUP_upg), and two ssGBLUP models with blending, tuning, and scaling parameters set to optimum values in constructing the inverse of the unified relationship matrix (ssGBLUP_adjusted). Realized prediction accuracies were highest for ssGBLUP_adjusted models (6–7% improvements compared to ssGBLUP). Accuracy of GEBVs for milk, protein, and fat yields ranged from 0.23, 0.29, and 0.30 for both ssGBLUP and ssGBLUP_Fx, 0.26, 0.32, and 0.34 for ssGBLUP_upg, and 0.29, 0.35, and 0.37 for ssGBLUP_adjusted models, respectively. Corresponding bias, expressed as regression coefficients, ranged from 0.30, 0.31, and 0.36 for ssGBLUP; 0.31, 0.32, and 0.37 for ssGBLUP_Fx; 0.41, 0.44, and 0.49 for ssGBLUP_upg; and 0.44, 0.47, and 0.53 for ssGBLUP_adjusted models, respectively. The improved accuracy and reduced bias observed with the ssGBLUP_adjusted underscores the importance of optimizing the blending of pedigree- and genome-based relationships to achieve more reliable GEBVs, thereby improving selection decisions in Holstein dairy cattle. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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19 pages, 1099 KB

Open AccessArticle

Growth, Health and Physiological Responses of Freshwater-Reared Atlantic Salmon (Salmo salar) Fed Graded Dietary Lipid Levels

by Byoungyoon Lee, Junoh Lee, Saeyeon Lim, Gwanghyeok Kim, Minjae Seong, Dahyun Jeong, Sijun Han, Byung-Hwa Min, Kang-Woong Kim, Seong-Mok Jeong, Mun Chang Park, Woo Seok Hong, Se Ryun Kwon and Youngjin Park

Animals 2026, 16(3), 356; https://doi.org/10.3390/ani16030356 (registering DOI) - 23 Jan 2026

Abstract

This study evaluated the optimal dietary lipid level for Atlantic salmon (Salmo salar) reared in freshwater, aiming to provide foundational knowledge for the development of cost-effective and nutritionally balanced aquafeeds. Four experimental diets were formulated to contain comparable crude protein levels [...] Read more.

This study evaluated the optimal dietary lipid level for Atlantic salmon (Salmo salar) reared in freshwater, aiming to provide foundational knowledge for the development of cost-effective and nutritionally balanced aquafeeds. Four experimental diets were formulated to contain comparable crude protein levels (47%) but graded lipid levels of 14% (L14), 16% (L16), 18% (L18), and 20% (L20), and were fed to salmon with an initial mean body weight of 241.5 ± 9.7 g during a 12-week feeding trial. Fish in the L16 group exhibited the highest weight gain (WG) and feed efficiency (FE), whereas those in the L14 group showed significantly reduced growth performance. Antioxidant analysis revealed that glutathione peroxidase (GPx) activity was lowest in the L14 group (p < 0.05), while plasma glucose concentration was minimized in the L16 group (p < 0.05). Transcriptomic profiling of liver tissue from the L14 and L16 groups identified 2117 differentially expressed genes (DEGs). Genes associated with lipid metabolism were more highly expressed in the L16 group, whereas immune- and inflammation-related genes were upregulated in the L14 group. These findings suggest that a dietary lipid level of approximately 16% is most favorable for promoting growth, metabolic stability, and overall health in freshwater-reared Atlantic salmon, thereby providing practical guidance for optimizing feed formulation and improving the economic efficiency of freshwater salmon aquaculture. Full article

(This article belongs to the Special Issue Advances in Nutrition, Sustainability and Ecology of Salmonids)

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23 pages, 328 KB

Open AccessArticle

Different Approaches to Caponisation of Cockerels and Their Relation to Welfare

by Alenka Dovč, Jurij Žel, Gordana Gregurić Gračner, Marko Cvetko, Veronika Budin, Zoran Žlabravec and Primož Klinc

Animals 2026, 16(3), 355; https://doi.org/10.3390/ani16030355 (registering DOI) - 23 Jan 2026

Abstract

The aim of this study was to improve surgical caponisation and identify stress factors associated with different pain management methods and post-operative periods. A total of 72 Prelux-G cockerels were caponised at six weeks of age. Eight experimental groups were established based on [...] Read more.

The aim of this study was to improve surgical caponisation and identify stress factors associated with different pain management methods and post-operative periods. A total of 72 Prelux-G cockerels were caponised at six weeks of age. Eight experimental groups were established based on caponisation status and pain management. Four groups were caponised using different pain management protocols (none, anaesthesia only, analgesia only, or both), while four non-caponised groups served as controls, including one group that received anaesthesia and analgesia without surgery. The remaining three groups served as non-caponised controls with varying levels of handling. The researchers monitored body weight, feed intake, respiratory and heart rate, vocalisations, response to pain, and depth of anaesthesia. The results confirmed that caponisation is painful, as reflected in increased physiological responses and vocalisations. The use of non-steroidal anti-inflammatory drugs alone did not provide effective pain relief. Additionally, the surgical procedure had no significant effect on weight gain or feed intake during the seven days following surgery. Stress levels, measured by blood serum corticosterone concentration, also increased during the procedure. The study concludes that anaesthesia significantly reduces pain and facilitates surgery, which is essential for improving animal welfare. Full article

(This article belongs to the Section Animal Welfare)

14 pages, 553 KB

Open AccessArticle

Comparative Metabolic and Stress-Related Responses to Adrenaline in Iberian and Landrace Pigs

by Manuel Lachica, Andreea Román, José Miguel Rodríguez-López, Lucrecia González-Valero, Consolación García-Contreras, Rosa Nieto and Ignacio Fernández-Fígares

Animals 2026, 16(3), 354; https://doi.org/10.3390/ani16030354 (registering DOI) - 23 Jan 2026

Abstract

Differences in metabolic traits between traditional and modern pig breeds may influence their physiological responses to stress hormones. This study evaluated the in vivo metabolic effects of an acute adrenaline challenge in Iberian (obese, slow-growing) and Landrace (lean, fast-growing) pigs (Sus scrofa [...] Read more.

Differences in metabolic traits between traditional and modern pig breeds may influence their physiological responses to stress hormones. This study evaluated the in vivo metabolic effects of an acute adrenaline challenge in Iberian (obese, slow-growing) and Landrace (lean, fast-growing) pigs (Sus scrofa domesticus). Four Iberian and five Landrace barrows (≈50 kg body weight; BW) fitted with a carotid catheter received an injection of adrenaline (3 µg/kg BW), and serial blood samples were collected for 105 min. Adrenaline transiently increased plasma glucose (p < 0.001) and lactate (p < 0.001) concentrations, both peaking at 5 min post-injection. Iberian pigs showed higher plasma lactate (1.26 vs. 1.03 mM; p = 0.002), triglycerides (0.34 vs. 0.27 mM; p < 0.001), and non-esterified fatty acids (NEFA; 0.38 vs. 0.29 mM; p = 0.021), but lower glucose (4.80 vs. 5.03 mM; p = 0.010) than Landrace pigs, while cholesterol remained unaffected (p > 0.10). No breed × time interaction was detected for any metabolite. The relative increase in glucose reached +47% in Iberian and +27% in Landrace pigs, whereas lactate rose +140% and +113%, respectively, indicating stronger glycolytic activation in Iberian pigs. Despite the limited sample size, the results provide physiologically relevant evidence supporting increased metabolic flexibility in Iberian pigs, characterized by a heightened sensitivity to adrenergic stimulation and associated with enhanced lipolytic and glycolytic responses; however, these conclusions should be interpreted within the specific experimental conditions under which the study was conducted. These findings demonstrate that Iberian pigs have higher metabolic sensitivity to adrenergic stimulation, with enhanced lipolytic and glycolytic activity. In conclusion, breed-dependent differences in stress-related metabolism suggest that Iberian pigs are furnished with increased metabolic flexibility to face short-term stress. Full article

(This article belongs to the Special Issue Impact of Genetics and Feeding on Growth Performance of Pigs—2nd Edition)

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22 pages, 3606 KB

Open AccessArticle

Body Coloration Characterization and Proteomic Analysis of Diurnal Color Variation in Farmed Larimichthys crocea

by Na Lin, Junjie Wu, Hongjin Deng, Jinli Wang, Banghong Wei, Yao Zheng and Quanyou Guo

Animals 2026, 16(3), 353; https://doi.org/10.3390/ani16030353 (registering DOI) - 23 Jan 2026

Abstract

The large yellow croaker (Larimichthys crocea) is an economically significant aquaculture species in Asia, with skin coloration being a key quality attribute affecting consumer choice and commercial value. This study integrated morphological, biochemical, and proteomic approaches to investigate chromatophore characteristics, pigment [...] Read more.

The large yellow croaker (Larimichthys crocea) is an economically significant aquaculture species in Asia, with skin coloration being a key quality attribute affecting consumer choice and commercial value. This study integrated morphological, biochemical, and proteomic approaches to investigate chromatophore characteristics, pigment composition, and diurnal body color variation in the large yellow croaker. Colorimetric analysis showed the highest yellowness, redness, and lightness values in ventral skin, followed by caudal skin, with dorsal skin showing the least yellowness. Three major chromatophores were identified: melanophores, xanthophores, and iridophores. Xanthophores were abundant in ventral and caudal skin, showing larger size and deeper pigmentation ventrally, while melanophores dominated dorsally and iridophores were mainly on scales. Skin and fins were key sites for carotenoid deposition, with lutein as the predominant carotenoid. Esters of lutein and zeaxanthin were the main contributors to yellow coloration in fish. A strong positive correlation was found between skin yellowness and total carotenoid content (R = 0.91, p < 0.05). The aggregation and dispersion of xanthosomes within xanthophores appeared to be the key driver behind the light-influenced diurnal body color variation. Proteomic analysis revealed motor proteins (such as KIF21, DYNC1L1, and MYO9) and pathways related to intracellular granule movement were probably related to the pigment transport in chromatophores of large yellow croaker. In addition, tubulin dynamics also appeared to participate in pigment translocation. This study is helpful to understand the pigmentary basis of this important farmed sea fish and provides a foundation for improving the golden color traits and further molecular research on diurnal color changes in large yellow croaker. Full article

(This article belongs to the Section Aquatic Animals)

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17 pages, 5442 KB

Open AccessArticle

Polymorphisms and Expression Characteristics of the ZSWIM7 Gene Are Associated with the Fertility of Male Allotetraploid of Red Crucian Carp × Common Carp

by Tao Dai, Minglin Dong, Siyang He, Weiling Qin, Conghui Yang and Yi Zhou

Animals 2026, 16(2), 352; https://doi.org/10.3390/ani16020352 (registering DOI) - 22 Jan 2026

Abstract

Allotetraploid fish produced by distant hybridization are valuable germplasm for the mass production of sterile triploids. The allotetraploid crucian–carp hybrid (4nAT, 4n = 200) is derived from the intergeneric cross between a female red crucian carp (Carassius auratus red var., 2n = [...] Read more.

Allotetraploid fish produced by distant hybridization are valuable germplasm for the mass production of sterile triploids. The allotetraploid crucian–carp hybrid (4nAT, 4n = 200) is derived from the intergeneric cross between a female red crucian carp (Carassius auratus red var., 2n = 100) and a male common carp (Cyprinus carpio L., 2n = 100). However, after 33 successive generations, this lineage faces a critical bottleneck in maintaining male fertility. The present study aimed to develop new biomarkers for testicular development and characterize the associated functional gene expression profile in 4nAT. Following whole-genome resequencing and selection signature analysis of 15 male 4nAT individuals from each of the high-development group (HDG) and low-development group (LDG), ZSWIM7 (Zinc Finger SWIM-Type Containing 7), a gene implicated in reproductive development, was selected as a candidate for further fertility association studies. Seven SNPs were screened in the coding region of ZSWIM7 of 70 4nAT males; among these, SNP3 (c.23T/C) exhibited a significant correlation between genotypes and testicular development: individuals with the CT genotype showed a higher gonadosomatic index (1.17 ± 0.68 vs. 0.65 ± 0.50) and greater counts of mature spermatozoa (2537.67 ± 283.95 vs. 341.56 ± 121.66) compared to those with the TT genotype. Further quantitative PCR and immunofluorescence assays demonstrated that ZSWIM7 was highly expressed in the testis and specifically localized to the nuclei of early meiotic primary spermatocytes. Collectively, these results establish ZSWIM7 as a promising biomarker for 4nAT testicular development, offering a potential molecular tool for maintaining male fertility in allotetraploid fish breeding. Full article

(This article belongs to the Special Issue Molecular Genetics in Aquaculture: Practical Applications for Sustainable Production)

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21 pages, 1681 KB

Open AccessArticle

Spatial Associations and Co-Occurrence Networks of Sympatric Species in an Asian Elephant Community

by Jingshan Wang, Xu Li, Yuan Tian, Wenguan Duan, Yuhui Si, Dusu Wen, Weibin Wang and Dehuai Meng

Animals 2026, 16(2), 351; https://doi.org/10.3390/ani16020351 (registering DOI) - 22 Jan 2026

Abstract

Understanding how species share resources (niche dynamics) and associate with each other is crucial for maintaining stable ecological communities. Using infrared camera traps, we constructed spatial association networks for an isolated Asian elephant population. The Asian elephant (Elephas maximus), a keystone [...] Read more.

Understanding how species share resources (niche dynamics) and associate with each other is crucial for maintaining stable ecological communities. Using infrared camera traps, we constructed spatial association networks for an isolated Asian elephant population. The Asian elephant (Elephas maximus), a keystone species in tropical forests, faces significant threats from habitat fragmentation and human disturbances, particularly in the isolated population of Nangunhe National Nature Reserve, Yunnan, China. Using infrared camera trapping, niche analysis, and interspecific association models, we examined the ecological role of Asian elephants and their sympatric species networks in fragmented habitats. We identified 44 species, including 11 species with higher relative abundance showing significant ecological correlations with elephants. Asian elephants exhibited the broadest spatial distribution, consistent with their role as ecological engineers due to high environmental tolerance and diverse resource utilization. Sympatric herbivores exhibited moderate spatial co-occurrence. Wild boars (Sus scrofa), red-bellied squirrels (Callosciurus erythraeus), northern pig-tailed macaques (Macaca leonina), and red junglefowl (Gallus gallus) demonstrated significant spatial associations with elephants. Lambda coefficient analysis revealed asymmetric associations reflecting spatial reliance of red-bellied squirrels and wild boars on elephant activity zones. Temporally, Asian elephants exhibited a stable bimodal activity pattern at dawn and dusk. Despite varying degrees of diel overlap with sympatric species, no significant temporal avoidance was detected, suggesting fine-scale coexistence mechanisms beyond the temporal dimension. We argue that conservation strategies are in urgent need of a transformation from single-species protection to the preservation of ecological interaction networks. This study clarifies the dominant position of Asian elephants in the community by mapping the spatial association networks between Asian elephants and sympatric species, and its findings hold substantial guiding significance for the recovery and protection of isolated Asian elephant populations. Full article

(This article belongs to the Section Ecology and Conservation)

18 pages, 1677 KB

Open AccessArticle

Exploration of Novel Markers in Tan Sheep Spermatogenesis

by Yuan Ma, Haoyan Jin, Nana Wang, Yaru Xie, Lingkai Zhang and Bei Cai

Animals 2026, 16(2), 350; https://doi.org/10.3390/ani16020350 (registering DOI) - 22 Jan 2026

Abstract

In livestock farming, the reproductive function and breeding performance of Tan sheep are crucial for enhancing farming efficiency. Despite advances in research on sheep germ cells, studies on the identification of markers for spermatogonia, spermatocytes, and spermatozoa in Tan sheep remain limited and [...] Read more.

In livestock farming, the reproductive function and breeding performance of Tan sheep are crucial for enhancing farming efficiency. Despite advances in research on sheep germ cells, studies on the identification of markers for spermatogonia, spermatocytes, and spermatozoa in Tan sheep remain limited and inadequate. In this study, Tan sheep were used as research subjects to investigate the morphological characteristics of testicular tissues, the developmental status of germ cells, and potential novel markers for spermatogonia, spermatocytes, and spermatozoa across different ages (0 days, 60 days, 180 days, and 365 days). Homology of the SMC3, G3BP1, and AKAP4 genes was analyzed via NCBI alignment. The localization and expression characteristics of these genes in the testis tissues of Tan sheep were investigated using HE staining, qPCR, and immunofluorescence double staining. The results showed that from 0 to 365 days of age, with increasing age, spermatogonia, spermatocytes, and spermatids exhibited an orderly distribution, and mature spermatozoa appeared in the tubular lumen, marking the initial establishment of the spermatogenic process. The homology of SMC3, G3BP1, and AKAP4 was 90%, 85%, and 81%. The mRNA levels of SMC3 and G3BP1 in the testes of 60-day-old Tan sheep were significantly increased, while AKAP4 expression showed a gradual increase with advancing age. SMC3 was co-localized with PLZF in undifferentiated spermatogonia, G3BP1 was co-expressed with SYCP2 in spermatocytes, and AKAP4 was co-expressed with PNA in spermatozoa. The findings of this study provide further supportive evidence for novel markers of spermatogonia, spermatocytes, and spermatozoa in Tan sheep. Full article

(This article belongs to the Special Issue Enhancing Male Animal Reproduction: Focus on Testicular Health, Semen Quality, and Fertility)

15 pages, 3033 KB

Open AccessArticle

Sonographic Assessment of Fetometric Parameters in Pigs of Different Prolific Genotypes for Gestational Age Estimation

by Frauke Janelt, Johannes Kauffold, Haukur Lindberg Sigmarsson, Ahmad Hamedy, Katharina Riehn, Martin Koethe, Jörg Altemeier and Philipp Maximilian Rolzhäuser

Animals 2026, 16(2), 349; https://doi.org/10.3390/ani16020349 (registering DOI) - 22 Jan 2026

Abstract

The slaughter of pregnant sows remains a relevant concern in modern swine production, with prevalence rates reported from 1.5–13% in Europe. Considering fetal sensitivity during late gestation and legal restrictions on transport and slaughter, reliable assessment of fetal age is of considerable practical, [...] Read more.

The slaughter of pregnant sows remains a relevant concern in modern swine production, with prevalence rates reported from 1.5–13% in Europe. Considering fetal sensitivity during late gestation and legal restrictions on transport and slaughter, reliable assessment of fetal age is of considerable practical, ethical, and legal relevance. In this study, 70 pregnancies from low-prolificacy (purebred German Saddleback) and medium-to-high prolificacy genotypes (purebred German Landrace and Duroc × German Landrace hybrids) were repeatedly examined using transabdominal ultrasonography, with a total of 15 examinations per pregnancy. Seven fetometric parameters—rosto-occipital distance, bi-parietal distance, orbital distance, sternum length, thorax diameter, body diameter, and crown–rump length—were measured in vivo, assessing two fetuses per pregnancy and calculating mean values to account for intra-individual variation. Parameter feasibility varied across gestation: during early gestation (gestation days 38 and 40), orbital distance, sternum length, and crown–rump length could be reliably measured; in mid-gestation, all seven parameters were measurable, whereas in late gestation (from gestational day 87 onward), crown–rump length was no longer measurable, and the remaining six parameters remained assessable for gestational age estimation. Crown–rump length (CRL) increased from a median of 3.2 cm (range 1.9–4.2 cm) at day 38 to 16.3 cm (range 14.0–18.2 cm) at day 77, representing the most practical parameter for determining the stage of gestation. Litter size had no significant effect on fetometric growth, except for a weak correlation with thorax diameter at day 77, and parity showed no measurable influence on any parameter. The results show that fetometric values in modern sow genotypes are smaller than those reported in earlier literature, highlighting the need for updated gestational age assessment. These findings provide practical guidance for gestational age estimation, supporting the enforcement of animal welfare legislation and potentially contributing to a reduction in the slaughter of highly pregnant sows. Full article

(This article belongs to the Section Animal Genetics and Genomics)

43 pages, 1026 KB

Open AccessReview

Insights into Non-Antibiotic Alternative and Emerging Control Strategies for Chicken Coccidiosis

by Rochelle A. Flores, Paula Leona C. Fletcher, Kyu-Yeol Son and Wongi Min

Animals 2026, 16(2), 348; https://doi.org/10.3390/ani16020348 (registering DOI) - 22 Jan 2026

Abstract

Coccidiosis, caused by an obligate intracellular parasite of the genus Eimeria, is the most economically parasitic disease in poultry. Long-term reliance on synthetic anticoccidials and ionophores has accelerated the emergence of drug resistance and intensified the need for effective, residue-free alternatives. This [...] Read more.

Coccidiosis, caused by an obligate intracellular parasite of the genus Eimeria, is the most economically parasitic disease in poultry. Long-term reliance on synthetic anticoccidials and ionophores has accelerated the emergence of drug resistance and intensified the need for effective, residue-free alternatives. This narrative review synthesizes findings from peer-reviewed studies published between 1998 and 2025, summarizing advances in non-antibiotic control strategies encompassing five domains: (i) phytochemicals and botanicals, (ii) functional nutrition and mineral modulators, (iii) microbial and gut modulators, (iv) host-directed immunological and biotechnological approaches, and (v) precision and omics-guided biotherapeutic platforms. These approaches consistently reduce lesion severity, oocyst shedding, oxidative stress, and mortality while improving growth parameters in a variety of Eimeria models. However, translation to field settings remains constrained by variable bioactive composition, limited standardization, inadequate pharmacokinetic data, and the scarcity of large-scale, multi-farm validation studies. This review provides a concise summary of current evidence and delineates critical knowledge gaps to guide the development, optimization, and deployment of next-generation anticoccidial strategies. Together, natural products and emerging biotechnologies provide a promising foundation for sustainable, high-welfare, antibiotic-independent coccidiosis control. Full article

(This article belongs to the Section Poultry)

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30 pages, 1426 KB

Open AccessFeature PaperArticle

Effects of Including Partially Destoned Olive Cake in Sheep Diet on Meat Quality and Salami Production

by Giuseppe Maniaci, Riccardo Gannuscio, Cristina Giosuè, Mahmood Ul Hassan, Gabriele Busetta, Elena Franciosi, Raimondo Gaglio, Massimo Todaro and Marco Alabiso

Animals 2026, 16(2), 347; https://doi.org/10.3390/ani16020347 (registering DOI) - 22 Jan 2026

Abstract

The valorization of cull sheep and the incorporation of agro-industrial by-products into animal feeding represent effective approaches to enhancing the sustainability of small ruminant production systems. This study investigated the effects of dietary inclusion of 17% partially destoned olive cake (OC) in the [...] Read more.

The valorization of cull sheep and the incorporation of agro-industrial by-products into animal feeding represent effective approaches to enhancing the sustainability of small ruminant production systems. This study investigated the effects of dietary inclusion of 17% partially destoned olive cake (OC) in the concentrate fed to Valle del Belice ewes on carcass characteristics, as well as on meat and salami quality. A 14-week feeding trial was conducted on 124 animals allocated to a control (CTR) and an experimental (EXP) group, balanced for parity, days in milk, and daily milk yield. At the end of the trial, five animals per group were slaughtered and their meat was processed into three types of salami: 100% sheep meat (SM), 90% sheep meat with 10% beef heifer brisket (HB), and 90% sheep meat with 10% pork backfat (PB). Meat and salami were evaluated for chemical composition, fatty acid profile, polyphenol content, antioxidant capacity, lipid oxidation, microbiological status, textural properties, and sensory characteristics. Dietary OC supplementation resulted in increased carcass weight, separable fat, intramuscular fat content, and monounsaturated fatty acids—particularly oleic acid—along with higher polyphenol levels and antioxidant activity. Salami produced from OC-fed ewes exhibited reduced weight loss during ripening, lower lipid oxidation, an improved MUFA/SFA ratio, and satisfactory sensory attributes. Microbiological analyses indicated a dominance of lactic acid bacteria and coagulase-negative staphylococci, with no pathogenic microorganisms detected. Overall, the inclusion of olive cake in the diet enhanced meat and processed product quality, supporting the valorization of olive oil by-products within circular economy frameworks. Full article

(This article belongs to the Section Animal Products)

45 pages, 9076 KB

Open AccessReview

Encephalitozoonosis in Pet Rabbits: Epidemiology, Pathogenesis, Immunology and Consensus on Clinical Management

by Emma Keeble, Frank Kϋnzel, Fabiano Montiani-Ferreira, Jennifer Graham, Edita Jeklová, Sari Kanfer, Angela Lennox, Guillaume Desoubeaux, Ethan Biswell, Carolyn Cray and Anja Joachim

Animals 2026, 16(2), 346; https://doi.org/10.3390/ani16020346 (registering DOI) - 22 Jan 2026

Abstract

Members of the microsporidial genus Encephalitozoon have the capacity to infect both mammals and birds, and E. cuniculi is most commonly found in rabbits. With a seroprevalence ranging up to 85%, E. cuniculi can be a problem in pet rabbits as well as [...] Read more.

Members of the microsporidial genus Encephalitozoon have the capacity to infect both mammals and birds, and E. cuniculi is most commonly found in rabbits. With a seroprevalence ranging up to 85%, E. cuniculi can be a problem in pet rabbits as well as in food production and laboratory animal science. While most infections are likely subclinical, there are three main clinical presentations: neurological, renal, and ocular. Typical clinical signs including vestibular disease and phacoclastic uveitis may develop with initial or relapsing infection, while renal infection is usually progressive and associated with non-specific clinical signs. High-sensitivity/specificity ante mortem diagnostic options are lacking, and serological testing most often provides adjunct rather than definitive information such that physical examination and other diagnostics are used more so for ruling out other differentials and comorbidities, rather than confirming infection. In the veterinary community, treatment regimens are variable given the lack of thorough studies and a consensus. The aim of this document is to present the available literature to give a concise review of this organism and its infection of rabbits as well as to propose guidelines and protocols for diagnostics and treatment regimens. In addition, the current challenges and recommendations for further studies are discussed. Full article

(This article belongs to the Special Issue Advances in Exotic Pet Medicine)

14 pages, 1467 KB

Open AccessArticle

BioControl 3.0: Biological Control Complex for Pest Control—Enhanced Control of Locusta migratoria manilensis via Combined Application of Metarhizium anisopliae var. acridum and Carabus smaragdinus

by Linqiang Gao, Yan Wang, Ruxin Wang, Jinshu Yang, Meiyi Yang, Yusheng Liu, Guangjun Wang, Mark R. McNeill, Zehua Zhang, Xinghu Qin and Haiyan Wang

Animals 2026, 16(2), 345; https://doi.org/10.3390/ani16020345 (registering DOI) - 22 Jan 2026

Abstract

Locusta migratoria manilensis (Meyen) is a highly destructive insect pest worldwide. However, excessive reliance on insecticides has resulted in significant environmental pollution. Biocontrol complexes combine two or more BCAs to address the limitations of individual agents. However, biocontrol complex for locust control has [...] Read more.

Locusta migratoria manilensis (Meyen) is a highly destructive insect pest worldwide. However, excessive reliance on insecticides has resulted in significant environmental pollution. Biocontrol complexes combine two or more BCAs to address the limitations of individual agents. However, biocontrol complex for locust control has been rarely reported. Here, we propose BioControl 3.0, which integrates Metarhizium anisopliae var. acridum (Driver and Milner) and Carabus smaragdinus (Fischer von Waldheim) for locust control. We evaluated this system through a series of laboratory bioassays and semi-field cage experiments, comparing single-agent applications, sequential combinations (BioControl 2.0), and predator-mediated delivery (BioControl 3.0), and quantified locust mortality and interaction effects between predation and infection We found that M. anisopliae caused >85% mortality of locust nymphs at 1 × 10⁸ conidia/mL (LT₅₀ ≈ 6 days) while exhibiting negligible virulence toward C. smaragdinus. BioControl 2.0 (sequential application) increased mortality compared to single agents. However, this approach revealed a significant negative interaction between predation and infection, which limited the total control efficacy. BioControl 3.0 (predator-vectored fungus) achieved the highest corrected mortality, with predation and infection acting independently and additively (no detectable antagonistic interaction). By leveraging a predatory vector, BioControl 3.0 decouples negative interaction and harnesses dual biotic pressures, offering a cost-effective, environmentally benign alternative to conventional locust control. Our findings provide a blueprint for designing integrated predator-pathogen complexes and optimizing deployment strategies for sustainable management of locust outbreaks. Full article

(This article belongs to the Section Ecology and Conservation)

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21 pages, 15965 KB

Open AccessArticle

Research on Seasonal Disease Warning Methods for Northern Winter Sheep Based on Ear-Base Temperature

by Jianzhao Zhou, Runjie Jiang, Dongsheng Xie and Tesuya Shimamura

Animals 2026, 16(2), 344; https://doi.org/10.3390/ani16020344 (registering DOI) - 22 Jan 2026

Abstract

The temperature at the base of the ear is highly correlated with the core body temperature of sheep and responds sensitively to febrile conditions, making it a valuable indicator of sheep health. In northern China, the closed housing environment during winter increases the [...] Read more.

The temperature at the base of the ear is highly correlated with the core body temperature of sheep and responds sensitively to febrile conditions, making it a valuable indicator of sheep health. In northern China, the closed housing environment during winter increases the incidence of seasonal diseases such as upper respiratory infections and pneumonia, which severely affect the economic efficiency of sheep farming. To address this issue, this study proposes an early-warning method for winter diseases in sheep based on ear-base temperature. Ear temperature, body weight, and environmental data were collected, and Random Forest was employed for feature selection. Bayesian optimization was used to fine-tune the hyperparameters of a one-dimensional convolutional neural network to construct a predictive model of ear-base temperature using data from healthy sheep. Based on the predicted normal range, an early-warning strategy was established to detect abnormal temperature patterns associated with disease onset. Experimental results demonstrated that the proposed method achieved a high detection rate for common winter diseases while maintaining a low false positive rate, and validation experiments confirmed its effectiveness under practical farming conditions. Combined with low-cost temperature-sensing ear tags, the proposed approach enables real-time health monitoring and provides timely early warnings for winter diseases in large-scale sheep farming, thereby improving management efficiency and economic performance. Full article

(This article belongs to the Section Animal System and Management)

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22 pages, 2485 KB

Open AccessArticle

Metabolomic Markers Reveal How hCG–Ketoprofen Intervention Increase Pregnancy Percentage Following Timed Artificial Insemination in Dairy Cows

by Hubdar Ali Kolachi, Muhammad Shahzad, Jesse Oluwaseun Ayantoye, Baigao Yang, Xiaomeng Zhang, Pengcheng Wan and Xueming Zhao

Animals 2026, 16(2), 343; https://doi.org/10.3390/ani16020343 (registering DOI) - 22 Jan 2026

Abstract

The objective of this study was to determine if the use of human chorionic gonadotrophin (hCG) and ketoprofen would affect the pregnancy percentages of dairy cows following timed artificial insemination (TAI). This experiment was conducted on a commercial dairy farm in China involving [...] Read more.

The objective of this study was to determine if the use of human chorionic gonadotrophin (hCG) and ketoprofen would affect the pregnancy percentages of dairy cows following timed artificial insemination (TAI). This experiment was conducted on a commercial dairy farm in China involving 799 healthy Holstein cows (2–4 parities) between October and December 2024. Cows were randomly assigned to three groups: hCG-3 = treated with (0 d: GnRH, 100 μg; 7–8 d: PGF_2α, 0.4 mg; 52 h: GnRH, 100 μg; 14–16 h: TAI) + hCG 3 vials (300 µg)/cow on day 7 of TAI; hCG-2 group = TAI + 2 vials (200 µg) hCG/cow on day 7; and hCG+ketoprofen = TAI + 300 µg hCG/cow + ketoprofen 10 mL/cow on days 15 and 16 of TAI. Metabolomic profiling (untargeted and targeted) of 22 pregnant cows was conducted on serum collected on days 17 and 21 post-TAI. Results indicated greater pregnancy percentages in the cows of the hCG+ketoprofen-treated group compared to those in the other two groups (60.1% compared with 49.6% and 41.9%). The cows treated with hCG+ketoprofen had less oxidative stress markers, downregulation of arachidonic acid metabolism and upregulation of glycerophospholipid metabolism on day 17 after TAI, indicating that there was upregulation of tryptophan and serotonergic pathways, increased amino acid metabolism and continued anti-inflammatory effects on day 21 after TAI. These findings were confirmed by evaluation data collected by conducting the targeted metabolomic procedures, as indicated by the greater progesterone and melatonin and lesser 17-estradiol and 21-deoxycortisol concentrations. These findings indicate that combined hCG+ketoprofen administrations following the TAI treatment regimen improve pregnancy percentages in dairy cattle as a result of metabolic and endocrine milieu modulations. Full article

(This article belongs to the Special Issue Advances in Dairy Cattle Reproduction: Second Edition)

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