Gastrointestinal (GI) parasites in small ruminants, especially goats and sheep, have caused significant socio-economic and public health challenges worldwide. The aim of the present study was to investigate the diversity and prevalence of GI parasites in goats and sheep in Jiangsu, Shaanxi and Hunan provinces of China, and to assess whether the age of animals, sampling season and feeding mode influence the distribution and infection of GI parasites. A total of 1,081 fecal samples collected from goats (n = 835) and sheep (n = 246) were detected by saturated saline flotation technique and nylon sifter elutriation and sieving method for eggs/oocysts, respectively. Based on the morphological observation of eggs and oocysts, one tapeworm, five nematodes, three trematodes and nineteen coccidia were identified, of which seven helminths belong to zoonotic parasites. The infection rate of parasites was 83.4% (902/1081) in total samples, 91.6% (765/835) in goats, and 55.7% (137/246) in sheep. The infection rate of coccidia was 71.0% (767/1081), and that of helminths was 56.2% (607/1081). The dominant species was E. alijeri (67.3%, 562/835) in goats, E. parva (30.1%, 74/246) in sheep. The highest prevalent helminths were Trichostrongylidae spp. in goats (58.3%, 487/835), and Moniezia spp. in sheep (22.76%, 56/246). Of 902 positive samples, 825 (91.5%, 825/902) contained multiple (2–10) parasites. The feeding mode, sampling season and regions were relevant risk factors which have significant influence on the occurrence of GI parasites in goats and sheep. The risk coefficient of parasite infection in autumn was 2.49 times higher than spring (Odds ratio = 2.49, 95% CI = 1.51–4.09, p < 0.001). Compared to raising on the high beds, the goats and sheep raising on the ground had the higher risk of parasite infection (OR = 3.91, 95% CI = 2.07–7.40, p < 0.001). The risk coefficient of parasite infection in Shaanxi and Hunan was 3.78 and 1.25 times higher than that in Jiangsu (OR = 3.78, 95% CI = 2.01–7.12, p < 0.001; OR = 1.25, 95% CI = 1.21–1.29, p < 0.001). These data are significant for the development of prevention strategies to minimise economic losses from small ruminant production and to reduce the risk of water and food infecting humans as vectors of zoonotic parasitic diseases.

With the growing demand for sheep, the sheep farming industry has developed rapidly. However, lamb diarrhea, a disease with high mortality rates, significantly hampers the industry’s growth. Traditional antibiotic treatments often disrupt the Intestinal microbiota, induce antibiotic resistance, and cause adverse side effects, highlighting the urgent need to develop alternative therapies. Bacteroides fragilis, a candidate next-generation probiotic, has been closely associated with intestinal health. This study investigated the growth characteristics and probiotic effects of a sheep-derived Bacteroides fragilis isolate, focusing on its efficacy in alleviating lamb diarrhea and infectious intestinal diseases. The experiments demonstrated that the Bacteroides fragilis isolate grows well under mildly acidic conditions (pH 6–8), exhibits some tolerance to bile salts, and has survival rates of 38.89% and 92.22% in simulated gastric and intestinal fluids, respectively, indicating its potential as a probiotic. In a mouse model, Bacteroides fragilis intervention significantly alleviated colonic inflammation caused by Enterohemorrhagic Escherichia coli infection, enhanced tight junction protein expression, mitigated oxidative stress, and improved intestinal barrier function, with high-dose interventions showing superior effects. In lamb trials, Bacteroides fragilis intervention stopped diarrhea in four out of five lambs, partially restored intestinal microbiota diversity, and reduced the abundance of potential pathogens such as Aerococcus suis and Corynebacterium camporealensis. Therefore, Bacteroides fragilis exhibited remarkable effects in regulating intestinal homeostasis, alleviating inflammation, and promoting recovery from diarrhea.

Sheep and goats serve as crucial hosts for Cryptosporidium spp. and are primarily responsible for its transmission via the fecal–oral route. This can result in symptoms such as lamb weight loss, diarrhea, and even fatalities, leading to significant economic losses. Currently, there is a lack of scholarly research investigating the prevalence of Cryptosporidium spp. infection in sheep and goats specifically within Jiangsu province. This study collected fecal samples from sheep and goats, extracted their DNA, amplified target bands using nested PCR, sequenced the DNA, constructed a phylogenetic tree, and identified the genetic genotype. In total, 3 positive samples were identified out of 398 samples. Furthermore, the gene sequences of these samples exhibited significant homology with C. xiaoi in GenBank. The phylogenetic analysis revealed that the Cryptosporidium spp. parasites under investigation are phylogenetically related to C. xiaoi. Conducting epidemiological investigations and accurately identifying the species of Cryptosporidium spp. is of utmost importance not only for the mutton sheep farming industry in Jiangsu but also for the proactive safeguarding of human health.

In order to investigate the infection status and genotypes of Enterocytozoon bieneusi (E. bieneusi) in sheep and goats in Jiangsu Province, a total of 786 fresh fecal samples from 18 farms across five regions in Jiangsu were collected and examined for the presence of E. bieneusi, and the genotype of E. bieneusi was examined using nested-PCR and sequencing of the ribosomal internal transcribed spacer. The results showed that E. bieneusi was detected in the fecal samples of sheep and goats in all regions, with infection rates ranging from 23.65% to 42.81%. The overall infection rate was 36.51% (287/786). The infection rate of E. bieneusi showed no significant difference between sheep and goats, as well as among different ages of animals (p > 0.05), but showed a significant difference in sheep and goats with different health conditions (p < 0.05). The positive products were amplified and cloned and subjected to sequenced analysis. Six genotypes, BEB6, CHG2, CHG3, CHC8, CHG14, and COS-I, were found. Phylogenetic analysis indicated that the six genotypes belonged to Group 2, which had previously been described as a non-zoonotic group.

Avian coccidiosis is an intestinal disease caused by Eimeria spp. infection. A deeper understanding of the interaction between host gut microbiota and the Eimeria parasite is crucial for developing alternative therapies to control avian coccidiosis. Here, we used full-length sequencing of 16S ribosomal RNA amplicons to compare changes in the gut microbiota of chickens infected with Eimeria tenella, Eimeria maxima, and Eimeria necatrix, aiming to identify both species-specific and common alterations in gut microbiota at 4 and 10 days post-infection. The result revealed that infection with all three Eimeria species led to a decrease in the abundance of the microbial genera Limosilactobacillus, Streptococcus, Alistipes, Lactobacillus and Phocaeicola, while the abundance of Bacteroides, Escherichia and Ligilactobacillus increased. Escherichia and Enterococcus were most abundant in the jejunum of the E. necatrix-infected group and in the cecum of the E. tenella-infected group, whereas Megamonas abundance was highest in the E. maxima-infected group. LEfSe analysis showed that infection with all three Eimeria species significantly reduced the abundance of 13 bacterial species, including Acetilactobacillus jinshanensis, Bacteroides ndongoniae, Barnesiella viscericola, Christensenella minuta, Enterocloster clostridioformis, Gemella haemolysans_A, Granulicatella adiacens, Lawsonibacter sp000177015, Limosilactobacillus reuteri, Limosilactobacillus reuteri_D, Limosilactobacillus vaginalis_A, Limosilactobacillus caviae, Limosilactobacillus vaginalis. Infection with E. tenella significantly increased the abundance of five bacterial species, including Bacteroides fragilis, Enterococcus cecorum, Helicobacter pylori, Methylovirgula ligni, and Phocaeicola sp900066445. Infection with E. maxima significantly increased the abundance of seven bacterial species, including Clostridioides difficile, Faecalibacterium prausnitzii, Mediterraneibacter torques, Muribaculum intestinale, Mediterraneibacter massiliensis, Phascolarctobacterium faecium, and Phocaeicola plebeius. Infection with E. necatrix significantly increased the abundance of seven bacterial species, including Alistipes sp900290115, Anaerotignum faecicola, Bacteroides fragilis_A, Escherichia coli, Harryflintia acetispora, Pseudoclostridium thermosuccinogenes, and Tidjanibacter inops_A. The results showed that Eimeria infection causes significant species- and time-dependent changes in the gut microbiota of chickens. These findings enhance our understanding of coccidiosis pathogenesis and offer potential targets for developing probiotics.

Floppy Kid Syndrome (FKS) is a common and serious disease in goats, with incidence rates ranging from 10 to 50% and mortality rates between 20 and 60%. This study aimed to investigate the etiology of FKS through blood biochemical analysis and metagenomic sequencing. Blood biochemical analysis revealed metabolic disorders in FKS-affected goats, including acidosis and hypoglycemia. Metagenomic analysis showed marked gastric and gut dysbacteriosis, characterized by an increase in pathogenic bacteria such as Escherichia coli and Staphylococcus aureus, alongside a significant reduction in probiotic like Lactobacillus amylovorus. Furthermore, species diversity and richness were notably lower in FKS-affected goats compared to healthy goats. Based on these findings, we infer that FKS is a multifactorial disease caused by gastric and gut dysbacteriosis. The immaturity of the digestive system in newborn goats, combined with environmental stressors (such as sudden changes in weather), leads to gastric and gut dysbacteriosis, with a significant reduction in probiotic and an overgrowth of pathogenic bacteria. The dysbacteriosis, along with the inability to properly digest excessive milk intake, contributes to the accumulation of undigested milk in the digestive tract, creating an environment conducive to pathogenic bacteria growth. The fermentation of milk and the production of excessive lactic acid by pathogenic bacteria are absorbed into the bloodstream, causing acidosis and hypoglycemia. These metabolic disorders, in conjunction with the dysbacteriosis and systemic dysfunction, lead to the onset of FKS. These results underscore the critical role of gastric and gut dysbacteriosis in the pathogenesis of FKS, highlighting the need for targeted preventive and therapeutic strategies.