Anaplasma phagocytophilum is an obligate intracellular, tick-borne bacterial pathogen capable of causing disease and even mortality in various mammals, including humans. Non-coding RNAs play important regulatory roles in multicellular organisms, including innate and adaptive immune pathways, which control bacterial, parasitic, and viral infections. However, the global transcriptomic landscape encompassing both ncRNAs and mRNAs in HL-60 cells invaded by A. phagocytophilum remains unexplored. Cell apoptosis was evaluated by flow cytometry at multiple time points after HL-60 cell infection with A. phagocytophilum. Total RNA was extracted and analyzed by RNA sequencing (RNA-seq) to delineate expression alterations of long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) at 24 h post-infection (hpi). Bioinformatics methods were employed for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses to elucidate the potential functions of these differentially expressed genes. Furthermore, an integrated bioinformatics approach was applied to systematically construct a competing endogenous RNA (ceRNA) network involving lncRNAs, miRNAs, and mRNAs. A. phagocytophilum infection accelerated HL-60 cell apoptosis at multiple time points, with the most significant effect observed at 24 hpi. Transcriptome profiling at 24 hpi identified substantial differential expression, including 487 lncRNAs, 550 mRNAs, and 22 miRNAs with statistically significant changes in expression. Then, expression patterns of eight lncRNAs, eight mRNAs, and seven miRNAs were experimentally validated through reverse transcription quantitative polymerase chain reaction (RT-qPCR), demonstrating strong correlation with RNA-seq results. Bioinformatics analyses revealed significant enrichment of differentially expressed mRNAs in three key pathways: the PI3K/Akt signaling pathway, the actin cytoskeleton regulation pathway and the p53 signaling pathway. Differentially expressed lncRNAs were largely related to the phospholipase D signaling pathway and pathways related to cortisol and aldosterone synthesis/secretion. The altered miRNAs showed predominant enrichment in Rap1 and NF-κB signaling pathways. Notably, computational reconstruction of the lncRNA–miRNA–mRNA ceRNA network identified hsa–miR–4518 and hsa–miR–3609 as central regulatory nodes. This comprehensive transcriptome study elucidates complex gene regulatory networks activated in HL-60 cells after A. phagocytophilum invasion, with particular emphasis on pathogen-modulated miRNA signatures that coordinate critical pathways governing host immune responses and microbial survival strategies. These findings elucidate previously uncharacterized molecular mechanisms underlying A. phagocytophilum pathogenesis and may provide actionable targets for novel therapeutics.

ABSTRACT Meat, as an important source of animal protein, has attracted widespread attention in recent years because of its quality and safety issues. Therefore, it is particularly important to assess potential impact risks and identify improvement strategies. This review comprehensively discusses the main factors influencing the meat quality, including genetic and environment factors. Furthermore, this review focuses on the application of nutritional and feed‐based strategies for improving the meat quality, including feed additives such as probiotics, prebiotics, plant extracts, antioxidants, and functional amino acids, which can markedly enhance the physicochemical properties, nutritional quality, and taste of meat by modulating the intestinal microecological balance, strengthening antioxidant defense mechanisms, and optimizing nutrient metabolism. These insights will help lay the foundation for promoting the high‐quality development of the lamb industry and implementing the One Health concept.

Membrane transporters play a vital role in the obligate intracellular parasite Toxoplasma gondii, mediating the acquisition of nutrients from host cells, the regulation of ion gradients, and the maintenance of metabolic homeostasis. Despite their central importance for parasite survival, pathogenesis, and drug resistance, the majority of T. gondii transporters remain poorly characterized. Key unresolved questions include the mechanisms underlying purine nucleotide transport across the plasma membrane and the import/export of metabolites for core pathways in the apicoplast (e.g., thiamine, isopentenyl diphosphate[IPP]/dimethylallyl diphosphate [DMAPP], and coproporphyrinogen III) and mitochondria (e.g., amino acids and cofactors). Recent advances in bioinformatics and CRISPR-based phenotypic screening have enabled systematic identification of transporter candidates. This review summarizes current knowledge of T. gondii transporters localized to the plasma membrane, apicoplast, mitochondria, endoplasmic reticulum, and Golgi apparatus, highlighting their roles in nutrient acquisition, metabolic crosstalk, and organellar function. Furthermore, we propose a screening strategy integrating transmembrane domain prediction, CRISPR phenotyping, and hyperLOPIT-based protein localization to prioritize uncharacterized transporters for functional study. These insights underscore the potential of transporters as therapeutic targets and provide a roadmap for future research into the physiology of T. gondii.

The global push to restrict antibiotic use in livestock has intensified the need for effective, safe feed additives, particularly for young lambs, which are highly susceptible to post-weaning diarrhea and immune dysfunction due to an underdeveloped intestinal barrier. Laminaria extract, rich in bioactive polysaccharides, has emerged as a promising candidate; however, its functional mechanisms in ruminants remain poorly understood. This study therefore investigated the effects of dietary Laminaria extract supplementation on growth performance, immune parameters, gut microbiota, and fecal metabolomic profiles in lambs. Lambs were randomly assigned to five groups: a basal control (CON), three Laminaria extract doses (LL, 1 g/kg; LM, 3 g/kg; LH, 6 g/kg), and a diclazuril positive control (DIC). Growth performance was evaluated via body weight and average daily gain (ADG). Serum immune cytokines were measured by ELISA, gut microbiota via 16S rRNA sequencing, and fecal metabolomics by UPLC–MS, followed by integrative correlation and pathway analyses. Dietary Laminaria supplementation improved growth performance and immune markers in a dose-dependent manner, with the high-dose (6 g/kg) group exhibiting the most pronounced effects. Specifically, the high-dose group showed a 217.47

IntroductionSanguinarine (SNG), a benzophenanthridine alkaloid derived from Macleaya cordata, exerts beneficial effects in monogastric animals; however, its mechanisms of action in ruminants remain poorly understood. This study aimed to explore whether dietary SNG supplementation improves growth performance and immune function in lambs via modulating gut microbiota and host metabolism.MethodsLambs received dietary SNG extract at 200 or 800 mg/kg body weight (equivalent to 4 and 16 mg/kg BW pure SNG, respectively). Growth performance, serum immune-antioxidant indices, gut microbiota, and metabolomics profiles were determined to evaluate the treatment effects.ResultsSNG supplementation significantly increased average daily gain, up-regulated serum IgG, IL-6 and IFN-γ, and down-regulated IL-4 and IL-10. Antioxidant enzyme activities decreased, whereas malondialdehyde concentration was not altered. Microbiota analysis showed reduced Blautia abundance and increased Monoglobus and Colidextribacter across both SNG-treated groups. Metabolomics revealed modified arachidonic acid (AA) metabolism, with elevated lipid mediators 15(S)-HpEPE and 20-hydroxy LTB4 in SNG-fed lambs. Integrative analysis identified a potential “Blautia-AA-immune” regulatory pattern: high-dose SNG induced a pro-inflammatory Th1-type response, while low-dose SNG sustained immune homeostasis through anti-inflammatory eicosanoids.DiscussionOur findings indicate that SNG improves growth performance and immune function in lambs by reshaping gut microbiota and reprogramming host lipid metabolism. This work provides mechanistic support for the application of SNG as a functional feed additive for ruminants.

Ticks and tick-borne pathogens pose significant threats to livestock and public health. While tick occurrences have been reported in China, systematic assessments of pathogen risk factors across diverse hosts and regions remain limited. This study investigated tick distribution, prevalence, and associated pathogen infections across seven sampling sites in China, analyzing 521 ticks collected from cattle, goats, sheep, dogs, and wild boars. Molecular identification revealed five tick species, with Haemaphysalis longicornis (58.93%, 307/521) and Rhipicephalus microplus (24.18%, 126/521) being the most prevalent, exhibiting distinct host and geographic preferences. Pathogen screening detected Anaplasma bovis (10.94%, 57/521), Anaplasma ovis (6.91%, 36/521), Anaplasma phagocytophilum (3.84%, 20/521), and Piroplasmida (1.34%, 7/521). Pathogen carriage rates varied significantly among regions (p < 0.05), with the highest in Haikou (45.83%, 44/96). Significant differences in pathogen carriage were observed among tick species (p < 0.05), with the highest rate in H. hystricis (37.14%, 13/35). The overall co-infection rate was 3.65% (19/521), predominantly driven by concurrent A. ovis and A. bovis infections (2.30%, 12/521), which may complicate diagnosis and exacerbate disease outcomes. Together, these findings highlight the complex interactions among tick vectors, vertebrate hosts, and pathogen communities across diverse regions of China, revealing host- and region-specific distribution patterns that provide critical evidence to strengthen integrated public health and veterinary surveillance and mitigate zoonotic threats at the human-animal-environment interface.

Coccidiosis is a global disease caused by protozoans, typically including Eimeria spp., which pose a significant threat to the normal growth and development of young animals. Coccidiosis affects mainly the gut, where parasite proliferation occurs. The intestinal barrier, which consists of chemical, mechanical, biological, and immune defences, plays a crucial role in protecting the host against pathogens, xenobiotics, and toxins present in the gastrointestinal tract. When animals ingest sporulated Eimeria spp. oocysts, these parasites primarily reproduce in the intestinal tract, causing damage to the structure and function of the intestine. This disruption of intestinal homeostasis adversely affects animal health. Numerous studies have also revealed that Eimeria-infected animals experience slower bone growth rates, inferior meat quality, reduced egg production and quality, as well as impaired growth and development. Therefore, the purpose of this review is to examine the underlying mechanisms through which Eimeria spp. regulate intestinal damage and disturb the balance of the internal environment. Specifically, this review will focus on their effects on the structural basis of the host intestine’s chemical, mechanical, biological and immune barriers. This understanding is crucial for the development of effective drugs to prevent the invasion of Eimeria spp. into the intestine, which is of paramount importance for maintaining host health.

Eimeria primarily infects the intestinal epithelial cells of livestock and poultry, disrupting gut microbiota and metabolism, which can result in diarrhea and weight loss. In severe cases, it can lead to hematochezia and even mortality. Modern intensive and large-scale farming practices, combined with the fecal-oral transmission of coccidia, create environments conducive to coccidial infections. Chemical control methods may lead to drug residues, drug resistance, toxic side effects, and other related issues. In contrast, Chinese herbal medicines typically exhibit multi-target, multi-pathway, and synergistic properties in disease resistance. In this study, the McMaster counting method was employed to assess the anti-coccidial effects of Houttuynia cordata (H. cordata) in its untreated forms (raw, water extract, and alcohol extract). The impact of these treatments on the intestinal microbiota and metabolites of lambs was examined using 16S rRNA gene sequencing technology and non-targeted metabolomics. The findings indicated that H. cordata reduced the excretion of intestinal coccidian oocysts in lambs. Notably, the alcohol extract of H. cordata (HA) significantly enhanced the average daily weight gain (ADG) and increased the abundance of unclassified Lachnospiraceae, Christensenellaceae R_7 group, and UCG_005. Additionally, metabolites such as 6-Deoxyerythronolide B, Parthenolide, and Bacilysin were highlighted for their potential significance. Overall, HA demonstrated superior anticoccidial effects and improved weight gain, likely due to the enhancement of beneficial microbiota and metabolites. This study provides a theoretical foundation for understanding the mechanisms by which Chinese herbal medicine combats coccidiosis through the modulation of intestinal microbiota and metabolism.

Mutton consumption is increasing due to its abundant nutritional elements and flavorful taste. However, sheep breeding is inevitably influenced by various factors, including feed mycotoxin contamination and parasitic infection. In this study, we investigated the effect of aflatoxin B1 (AFB1) and Eimeria ovinoidalis (EO) on sheep meat quality following a two-week treatment. The results showed that oxidative stress triggered by EO or AFB1 in feed could cause significant changes in meat quality. Metabolomics and transcriptomics further revealed that the alteration in mutton quality is closely associated with glycolysis mediated by the hypoxia inducible factor-1α (HIF-1α) pathway. Interestingly, the glycolytic enzyme hexokinase 2 (HK2), a downstream gene of the HIF-1α pathway, exhibits a strong affinity for AFB1 and its metabolites, as revealed by molecular docking analysis, which is associated with a change in mutton quality-related indices. These findings provide novel insights that Eimeria or/and AFB1 compromise mutton quality by disrupting the HIF-1α/HK2/glycolysis axis.

Coccidia are among the primary pathogens causing diarrhea and even fatalities in lambs. With the increasing use of chemical drugs to treat coccidiosis, the problem of drug resistance is becoming more and more threatening. Therefore, there is an urgent need to identify novel alternative drugs for the treatment of the lamb coccidia. In this study, the effect of different doses and extraction methods of Artemisia annua (A. annua) on anticoccidial activity and growth performance was assessed by oocysts output (OPG), fecal index, average daily gain (ADG) and the new production value of experimental lambs. High-throughput sequencing technology was employed to investigate the effect of A. annua on the intestinal microbiota and metabolites of lambs afflicted with coccidiosis. The results revealed that all A. annua treatment groups exhibited good anticoccidial effects. According to the soft stool index and ADG analysis, the Low-dose A. annua (AL) and A. annua alcohol extract (AA) groups demonstrated a better overall effect. The microbiota and metabolites of lambs changed after A. annua was administered. Unclassified_Muribaculaceae exhibited a significant positive correlation with ADG (P < 0.05) and a negative correlation with OPG, although the latter was not statistically significant (P > 0.05). Alistipes displayed a significant negative correlation with ADG (P < 0.05), and a positive correlation with OPG (P > 0.05). Additionally, UCG 005 exhibited a highly significant negative correlation with OPG (P < 0.01). The above results demonstrated that AL and AA groups had more effective anticoccidial action. Unclassified_Muribaculaceae could be employed as a suitable probiotic to enhance weight gain in lambs, while UCG-005 could inhibit intestinal Eimeria colonization in lambs. Alistipes may serve as a biomarker for predicting the risk of intestinal coccidia outbreaks in lambs. A. annua induced significant changes in gut microbiota, accompanied by corresponding changes in metabolites. These differences in gut microbiota and metabolites provide valuable insights for subsequent research on the mechanisms underlying anticoccidial action.

Background: The gut health of livestock and poultry is of utmost importance as it significantly impacts their growth performance, disease resistance, and product quality. With the increasing restrictions on antibiotic use in animal husbandry, probiotics, prebiotics, synbiotics, and postbiotics (PPSP) have emerged as promising alternatives. This review comprehensively summarizes the roles of PPSP in promoting gut health in livestock and poultry. Results: Probiotics, such as Lactobacillus, Bifidobacterium, and Saccharomyces, modulate the gut microbiota, enhance the gut barrier, and regulate the immune system. Prebiotics, including fructooligosaccharides, isomalto-oligosaccharides, galactooligosaccharides, and inulin, selectively stimulate the growth of beneficial bacteria and produce short-chain fatty acids, thereby improving gut health. Synbiotics, combinations of probiotics and prebiotics, have shown enhanced effects in improving gut microbiota and animal performance. Postbiotics, consisting of inanimate microorganisms and their constituents, restore the gut microbiota balance and have anti-inflammatory and antibacterial properties. Additionally, the review looks ahead to the future development of PPSP, emphasizing the importance of encapsulation technology and personalized strategies to maximize their efficacy. Conclusions: Our aim is to provide scientific insights for PPSP to improve the gut health of livestock and poultry.

BackgroundSheep coccidiosis could disturb the balance of intestinal microbiota, causing diarrhea, and even death in lambs. Chemical drugs are the primary method of treating sheep coccidiosis, but their use will bring drug resistance, toxic side effects, drug residues, and other problems. Chinese herbal medicines are investigated as alternative methods for controlling coccidian infections.MethodsIn this study, the effect of fermented Artemisia annua (FA) on oocysts per gram (OPG), average daily gain (ADG), and expression of inflammatory factors were investigated in lambs that were naturally infected with coccidia.ResultsThe results showed that the FA had similar anti-coccidiosis effect to the original drug, while the FA demonstrated a more significant effect on weight gain, and a better ability to reduce the inflammatory response compared to the unfermented drug during the treatment period (P < 0.05). Furthermore, High-throughput sequencing technology was used to study the effects of FA on intestinal microbiota, and fecal metabolites of naturally infected lambs. The species richness of intestinal microbiota of lambs was significantly improved by FA. The abundance of bacteria unclassified_Muribaculaceae, and UCG_005 were increased by fermentation of A. annua. The abundance of bacteria Escherichia_Shigella, unclassified_Clostridia_UCG_014, and Alistipes was reduced. The prevention, and treatment of coccidiosis by fermentation of A. annua may also be related to a series of metabolites affected by intestinal microbiota, including artemisinin, Lysyl-Proline, and TRP-tyrosine.ConclusionFA was found to have superior anti-coccidiosis, anti-inflammatory, and weight gain effects compared to the original Artemisia annua. Intestinal microbes and metabolites such as unclassified_Muribaculaceae, UCG-005, and Artemisinin were identified, suggesting their potential significance. Alistipes was proposed as a biomarker for predicting intestinal coccidia outbreak risk in lambs, pending further validation. The correlation between microbiota, and metabolites may provide new insights into pathogenic changes associated with Eimeria spp.

AbstractThe intestinal tract is the main place for animals to digest food and absorb nutrients, which also serves as the first line of defense against pathogens that invade the internal environment. Therefore, normal intestinal structure and function are essential for animal health. Poultry coccidiosis is an intestinal disease primarily caused by the parasitization of intestinal epithelial cells by protozoa of the genus Eimeria. The occurrence of coccidiosis not only compromises the intestinal integrity of poultry but also increases their disease susceptibility, thus posing a serious threat to the overall health and productivity of poultry. Nowadays, the primary methods for controlling and preventing coccidiosis in poultry are anticoccidial drugs or live oocyst vaccines. However, the use of the former may be associated with problems of resistance and drug residues, while the use of the latter may cause intestinal damage and significantly increase farming costs. For these reasons, it is critical to investigate green, safe, and cost‐effective natural alternative strategies such as phytochemicals and probiotics for controlling coccidiosis as well as mitigating the deleterious effects of coccidial infections in production. In this review, we aim to summarize the role, mechanisms, and therapeutic potential of natural products in the treatment of coccidiosis to lay a theoretical foundation for effective coccidiosis control.

Cryptosporidium parvum is an important zoonotic pathogen that is studied worldwide. MicroRNAs (miRNAs) act as post-transcriptional regulators and may play a key role in modulating host epithelial responses following Cryptosporidium infection. Our previous study has shown that C. parvum downregulates the expression of miR-181d through the p50-dependent TLRs/NF-κB pathway. However, the mechanism by which miR-181d regulates host cells in response to C. parvum infection remains unclear. The present study found that miR-181d downregulation inhibited cell apoptosis and increased parasite burden in HCT-8 cells after C. parvum infection. Bioinformatics analysis and luciferase reporter assays have shown that BCL2 was a target gene for miR-181d. Moreover, BCL2 overexpression and miR-181d downregulation had similar results. To further investigate the mechanism by which miR-181d regulated HCT-8 cell apoptosis during C. parvum infection, the expression of molecules involved in the intrinsic apoptosis pathway was detected. Bax, caspase-9, and caspase-3 expression was decreased at 4, 8, 12, and 24 hpi and upregulated at 36 and 48 hpi. Interfering with the expression of miR-181d or BCL2 significantly affected the expression of molecules in the intrinsic apoptosis pathway. These data indicated that miR-181d targeted BCL2 to regulate HCT-8 cell apoptosis and parasite burden in response to C. parvum infection via the intrinsic apoptosis pathway. These results allowed us to further understand the regulatory mechanisms of host miRNAs during Cryptosporidium infection, and provided a theoretical foundation for the design and development of anti-cryptosporidiosis drugs.

In order to establish a stable in vitro culture platform for chicken small intestine three-dimensional (3D) organoids, in this study, crypt cells were collected from the small intestine of 18-day-old embryos of AA broilers. On the basis of the L-WRN conditioned medium, we optimized the culture conditions of chicken small intestinal organoids by adjusting the proportions of nicotinamide, N-acetylcysteine, LY2157299, CHIR99021, Jagged-1, FGF, and other cytokines to select the medium suitable for the long-term stable growth of the organoids. The optimization results showed that the addition of 1.5 µmol/L CHIR99021 significantly improved the organoid formation efficiency and organoid diameter. When 0.5 µmol/L Jagged-1 was added, a small amount of bud-like tissue appeared in organoids. After the addition of 50 ng/mL FGF-2, the rate of organoid germination was significantly increased. The 1.5 µmol/L CHIR99021, 0.5 µmol/L Jagged-1, and 50 ng/mL FGF-2 added in the medium can cooperate with each other to improve the formation and speed up the proliferation and differentiation of organoids, while improving the stemness maintenance of cells. The morphology, cell types, and culture characteristics of chicken small intestinal organoids were studied by HE staining, transmission electron microscopy, reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR), indirect immunofluorescence, and immunohistochemistry. The results showed that the 3D organoids of the chicken small intestine cultured in vitro were morphologically consistent with the chicken intestinal tissue and contained differentiated epithelial cells. In summary, we successfully established an in vitro culture system for chicken small intestinal organoids, providing a new method for the subsequent research on chicken intestinal physiology, pathology, and host-pathogen interaction mechanism and the development of relevant drugs.

The objective of the present study was to develop a real-time PCR (qPCR) technique for the diagnosis of Eimeria spp. in Ovis aries and Capra hircus. The qPCR technique was developed using SYBR Green, resulting in a PCR with high sensitivity, specificity, and reproducibility.

Meat from sheep offers an abundance of essential amino acids and trace elements essential for optimal human health and a delectable culinary delight. Because it has fewer calories and a lower cholesterol content than other meats, this succulent meat is not only delicious but also a nutritious choice. Globally, discriminating consumers have expressed profound appreciation for its irresistible flavor and nutritious composition. High-quality sheep breeds and lamb quality are in the spotlight as the market for sheep meat grows. Nevertheless, the demand for rapid growth and the use of antibiotics and other drugs have led to a shortage of high-quality mutton on the market. In the face of this emergency phenomenon, people add organic matter to the growth of mutton to improve the quality of mutton. This paper discusses the comprehensive evaluation methods of meat quality; summarizes the relationship between the nutritional components of meat and diet; discusses the genetic factors affecting meat quality attributes; feed nutrition, feeding methods, mutton storage methods, and related measures to improve the quality of mutton; and provides information on the current status of mutton and the challenges of ensuring high-quality meat supply in the future.

Coccidia of the genus Eimeriaare important pathogens that cause coccidiosis in livestockand poultry. Due to the expansion of intensive farming, coccidiosis has become more difficult to control. In addition, the continued use of anti-coccidiosis drugs has led to drug resistance and residue. Some herbs used in traditional Chinese medicine (TCM) have been shown to alleviate the clinical symptoms of coccidiosis, while enhancing immunity and growth performance (GP) of livestock and poultry. Previous in vitro and in vivo studies have reported that the TCM herb Portulaca oleracea exhibited anti-parasitic activities. In total, 36 female Hu lambs were equally divided into six treatment groups: PL (low-dose P. oleracea), PH (high-dose P. oleracea), PW (P. oleracea water extract), PE (P. oleracea ethanol extract), DIC (diclazuril), and CON (control). The treatment period was 14 days. The McMaster counting method was used to evaluate the anti-coccidiosis effects of the different treatments. Untargeted metabolomics and 16S rRNA gene sequencing were used to investigate the effects of treatment on the gut microbiota (GM) and GP. The results showed that P. oleracea ameliorated coccidiosis, improved GP, increased the abundances of beneficial bacteria, and maintained the composition of the GM, but failed to completely clear coccidian oocysts. The Firmicutes to Bacteroidesratio was significantly increased in the PH group. P. oleracea increased metabolism of tryptophan as well as some vitamins and cofactors in the GM and decreased the relative content of arginine, tryptophan, niacin, and other nutrients, thereby promoting intestinal health and enhancing GP. As an alternative to the anti-coccidiosis drug DIC, P. oleraceaeffectively inhibited growth of coccidia, maintained the composition of the GM, promoted intestinal health, and increased nutrient digestibility.

Abstract Sheep and goat coccidiosis has a worldwide distribution and is an important disease on lambing farms. Infection with multiple Eimeria species can lead to severe intestinal damage in sheep/goats and economic losses on farms. Disease is a serious constraint to the healthy development of small ruminant farming. Studies published on PubMed, CNKI, VIP, Wanfang and the resulting references of selected studies were included. Risk factors affecting prevalence were analyzed and stratified by geographic location and climatic variables, age, sex, feeding model, season, sample year, breeds and environment. The total prevalence of coccidia in sheep and goats reached more than 60% in most regions, in which the dominant species in sheep were mainly E. parva, E. ovinoidalis, and E. parva and E. ahsata. East China had the lowest prevalence of coccidia infection in sheep (43.24%), and the dominant species were different from those in the other regions, mainly E. bakuensis and E. gonzalezi. Southwestern China and Central China had slightly less than 40.0% goat coccidia infection, and the dominant species in goats were mainly E. arloingi, E. aligevi, E. hirci and E. ninakohlyakimovae. Sheep/goats of different ages can be infected with coccidiosis, but lambs between 1 and 3 months of age are more susceptible to the disease. When lambs become infected, the pathogen spreads rapidly throughout the herd. Spring, summer and autumn are the seasons with a high incidence of this disease. Environmental pollution may be a significant factor in the development of coccidiosis in sheep raised in large-scale housing. This study provides a comprehensive overview of the species, morphology and geographic distribution of Eimeria species in sheep and goats, summary prevalence in different regions of China, risk factors affecting prevalence, and prevention and control strategies.

The apicomplexan Eimeria ovinoidalis is distributed worldwide. It can cause clinical coccidiosis, which is one of the most pathogenic species in sheep, reducing growth rates and resulting in significant economic losses in the industry. Its principal clinical sign is profuse diarrhoea in young animals. In this study, we established a model of E. ovinoidalis infection in lambs to understand its pathogenicity and evaluate the gut microbiota and fecal metabolite profiles. Specifically, we observed a significant shift in the abundance of bacteria and disrupted metabolism in lambs. Especially during the peak period of excrete oocysts, it promoted the reproduction of some harmful bacteria in Proteobacteria and Actinobacteriota, and reduced the abundance of beneficial bacteria such as Lachnospiraceae and Rikenellaceae. In the later stage of the patent period, the abundance of harmful bacteria in the intestine decreased, the abundance of beneficial bacteria which could produce anti-inflammatory substances began to increase, and the abundance and diversity of intestinal flora also tended to parallel with the control group. Coccidia infection could lead to the increase of differential metabolites and metabolic pathways between infected and control group, but the difference decreased with time. During the peak period of excrete oocysts, although the antimicrobial metabolites such as Lividamine were up-regulated, the excess of these metabolites could still induce the production of endotoxin, while Butanoic acid and other anti-inflammatory metabolites decreased significantly. A metabolomics analysis showed that E. ovinoidalis infection altered metabolites and metabolic pathways, with biosynthesis of unsaturated fatty acids, Teichoic acid biosynthesis and Butanoate metabolism as the major disrupted metabolic pathways. Details of the gut microbiota and the metabolome after infection with E. ovinoidalis may aid in the discovery of specific diagnostic markers and help us understand the changes in parasite metabolic pathways.