Landscapes of Enteric Virome Signatures in Early-Weaned Piglets

The role of visfatin in peripheral immune organs and intestines of weaned piglets under lipopolysaccharide induced immune stress

To investigate the regulatory mechanisms and pathways of visfatin under immune stress injury in weaned piglets, we established a lipopolysaccharide-induced immune stress model in weaned piglets to study how visfatin affects peripheral immune organs and intestinal function. The results revealed that visfatin improved the inflammatory response in immune-stressed weaned piglets by reducing the levels of pro-inflammatory cytokines interleukin-1β, interleukin-6 and monocyte chemoattractant protein-1, as well as decreasing the neutrophil/lymphocyte ratio. Visfatin ameliorated oxidative stress in piglets by promoting the expression of superoxide dismutase and glutathione peroxidase. It also enhanced cell proliferation in peripheral immune organs (spleen and mesenteric lymph nodes) and suppressed cell apoptosis in these organs through the death receptor apoptosis pathway, thereby improving the immune function of weaned piglets under immune stress. Moreover, it alleviated intestinal villi damage, increased the abundance of beneficial bacteria, and elevated the levels of short-chain fatty acids, thus preserving the intestinal barrier's integrity and the balance of intestinal microbiota. Hence, these data indicate that visfatin can ameliorate immune stress injury in weaned piglets by exerting anti-inflammatory and antioxidant effects, enhancing immune organ and intestinal function.

Chinese Herbal Medicines as Natural Alternative Products to Antibiotics in Weaned Piglets through Intestinal Microbiota Regulation

During the growth process of weaned piglets, digestive problems such as gastrointestinal disorders and diarrhea are common. Farmers usually use antibiotics to help piglets grow smoothly. However, the overuse of antibiotics can lead to antibiotic resistance issues. Therefore, this study chose to use plant extracts as feed additives to explore their potential as alternatives to antibiotics. Additionally, Tilmicosin was used as the antibiotic because it is widely used in treating respiratory infections in piglets. Since traditional Chinese medicine often uses natural products, we selected Guizhi Li-Zhong (GLZ) extract as an alternative to antibiotics. The experiment involved 126 piglets, each 4 weeks old, which were randomly assigned to one of four groups: the sham group (basal diet without supplements, 10.3 ± 0.4 kg, n = 31), the low-dose GLZ group (basal diet with 0.05% GLZ, 10.9 ± 0.4 kg, n = 32), the regular-dose GLZ group (basal diet with 0.2% GLZ, 10.6 ± 0.4 kg, n = 32), and the regular-dose Tilmicosin antibiotic group (basal diet with 0.2% Tilmicosin, 10.2 ± 0.3 kg, n = 31). We recorded and compared the survival rate, growth rate, feed conversion ratio, and diarrhea incidence among four groups of weaned piglets from the 4th to the 10th weeks of age. Then, we examined the oxidative stress, inflammation, and apoptosis in small intestine tissue (jejunum and ileum) through immunohistochemistry and Western blot and compared the gut microbiota in large intestine tissue (colon and rectum) through a next-generation sequencing (NGS) analysis. Our results showed that weaned piglets supplemented with 0.05% and 0.2% GLZ had better survival rates, growth rates (p < 0.01), and feed conversion ratios (p < 0.01) compared to those receiving sham treatment. Even weaned piglets supplemented with 0.2% GLZ performed better than those supplemented with 0.2% Tilmicosin antibiotics (p < 0.05). Furthermore, the incidence of diarrhea and small intestine injury (indicated by oxidative stress-, inflammation-, and apoptosis-related proteins) in piglets supplemented with 0.05% and 0.2% GLZ was lower than in piglets receiving sham treatment (p < 0.05). Even piglets supplemented with 0.2% GLZ had less injury than those supplemented with 0.2% Tilmicosin antibiotics (p < 0.05). The NGS results further showed that GLZ treatment significantly improved beneficial bacteria in weaned piglets (p < 0.05), while antibiotic treatment reduced beneficial bacteria (p < 0.05). In summary, we recommend adding GLZ to the feed as an alternative to antibiotics. This not only effectively reduces intestinal damage but also improves the gut microbiota, thereby promoting the growth of weaning piglets.

Massive expansion of the pig gut virome based on global metagenomic mining

The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai-Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude ≈ 3000 m) across three critical developmental stages, including lactation, nursery, and fattening. The composition of viral communities in the Tibetan pig intestine, with a dominant presence of Microviridae phages observed across all stages of development, in combination with the previous literature, suggest that it may be associated with geographical locations with high altitude. Functional annotation of viral operational taxonomic units (vOTUs) highlights that, among the constantly increasing vOTUs groups, the adaptability of viruses to environmental stressors such as salt and heat indicates an evolutionary response to high-altitude conditions. It shows that the lactation group has more abundant viral auxiliary metabolic genes (vAMGs) than the nursery and fattening groups. During the nursery and fattening stages, this leaves only DNMT1 at a high level. which may be a contributing factor in promoting gut health. The study found that viruses preferentially adopt lytic lifestyles at all three developmental stages. These findings not only elucidate the dynamic interplay between the gut virome and host development, offering novel insights into the virome ecology of Tibetan pigs and their adaptation to high-altitude environments, but also provide a theoretical basis for further studies on pig production and epidemic prevention under extreme environmental conditions.

Prospects and Challenges of Bacteriophage Substitution for Antibiotics in Livestock and Poultry Production

The overuse and misuse of antibiotics in the livestock and poultry industry has led to the development of multi-drug resistance in animal pathogens, and antibiotic resistance genes (ARGs) in bacteria transfer from animals to humans through the consumption of animal products, posing a serious threat to human health. Therefore, the use of antibiotics in livestock production has been strictly controlled. As a result, bacteriophages have attracted increasing research interest as antibiotic alternatives, since they are natural invaders of bacteria. Numerous studies have shown that dietary bacteriophage supplementation could regulate intestinal microbial composition, enhance mucosal immunity and the physical barrier function of the intestinal tract, and play an important role in maintaining intestinal microecological stability and normal body development of animals. The effect of bacteriophages used in animals is influenced by factors such as species, dose, and duration. However, as a category of mobile genetic elements, the high frequency of gene exchange of bacteriophages also poses risks of transmitting ARGs among bacteria. Hence, we summarized the mechanism and efficacy of bacteriophage therapy, and highlighted the feasibility and challenges of bacteriophage utilization in farm animal production, aiming to provide a reference for the safe and effective application of bacteriophages as an antibiotic alternative in livestock and poultry.

Characteristics of the Fecal Microbiome of Piglets with Diarrhea Identified Using Shotgun Metagenomics Sequencing

Diarrhea in piglets is one of the most common diseases leading to high mortality and, as a result, to economic losses. Shotgun metagenomic sequencing was performed on the DNBSEQ-G50, MGI system to study the role of the fecal microbiome in the development of diarrhea in newborn piglets. Analysis of the study data showed that the composition of the fecal microbiome at the level of bacteria and fungi did not differ in piglets with diarrhea from the healthy group. Bacteria belonging to the phyla Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria were the most abundant. However, a higher level of bacterial alpha diversity was observed in the group of piglets with diarrhea, which may be due to dysbacteriosis and inflammation. The study of the virome showed the difference between the two types of phages: Bacteroides B40-8 prevailed in diseased piglets, while Escherichia virus BP4 was found in greater numbers in healthy piglets. The results of our study suggest that the association between the fecal microbiome and susceptibility to diarrhea in suckling piglets may have been previously overestimated.

Combining 16S rRNA Sequencing and Metabolomics Data to Decipher the Interactions between Gut Microbiota, Host Immunity, and Metabolites in Diarrheic Young Small Ruminants

Diarrhea is associated with gut microbiota, immunity, and metabolic alterations in goat kids and lambs. This study used 28 lambs (11 healthy and 17 diarrheic) and 20 goat kids (10 healthy and 10 diarrheic) to investigate the association between diarrhea occurrence and changes in gut microbiota, metabolism, and immunity in goat kids and lambs. The results revealed that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla in goat kids and lambs. In addition, Enterobacteriaceae and Lachnospiraceae families were identified in both diarrheic goat kids and lambs. Furthermore, functional prediction of microbiota showed that it was involved in cell motility and cancer pathways. The identified differential metabolites were implicated in the bile secretion pathway. Lambs had significant differences in immunoglobulin G (IgG), immunoglobulin M (IgM), interleukin-1β (IL-1β), and tumor necrosis factor-alpha (TNF-α) compared to goat kids. IgG and IL-1β were positively correlated to Patescibacteria, Clostridiaceae, and unclassified_Muribaculaceae in both diarrheic goat kids and lambs. In addition, weighted gene co-expression network analysis (WGCNA) revealed that the MEgreen module was positively associated with IgG, IgM, IL-1β, TNF-α, and triglyceride (TG). In conclusion, our results characterized the gut microbiota, metabolism, and immune status of lambs and goat kids suffering from diarrhea.

Longitudinal Investigation of Enteric Virome Signatures from Parental-Generation to Offspring Pigs

To date, studies on the swine gut microbiome have focused almost exclusively on bacteria. Despite recent advances in the understanding of the swine gut bacteriome at different growth stages, a comprehensive longitudinal study of the lifetime dynamics of the swine gut virome is lacking. Here, we used metagenomic sequencing combined with bioinformatic analysis techniques to characterize the gut viromes of parental-generation and offspring pigs at different biological classification levels. We collected 54 fecal samples from 36 parental-generation pigs (18 breeding boars [Duroc] and 18 pregnant/lactating sows [Landrace]) and 108 fecal samples from 18 offspring pigs during the lactation (day 3), nursery (days 26, 35, and 49), growing (day 120), and finishing (day 180) stages. Alpha diversity, including community richness (richness index) and diversity (Shannon index), showed an overall increasing trend in offspring pigs. Distinct shifts (beta diversity) in the microbiome structure along different growth stages were observed. The linear discriminant analysis effect size (LEfSe) algorithm revealed 53 viral genus that are stage specific. Host prediction results showed that enteric viruses are probably correlated with carbohydrate decomposition. We identified abundant auxiliary carbohydrate-active enzyme (CAZyme) genes from enteric viruses, most of which are glycoside hydrolase genes and participate in the biolysis of complex polysaccharides. IMPORTANCE This study shows that distinct stage-associated swine gut viromes may be determined by age and/or gut physiology at different growth stages, and enteric viruses probably manipulate carbohydrate decomposition by abundant glycoside hydrolases. These findings fill a gap in the longitudinal pattern of the swine gut virome and lay the foundation for research on the function of swine enteric viruses.

Metagenomic Sequencing Identified Specific Bacteriophage Signature Discriminating between Healthy and Diarrheal Neonatal Piglets

Neonatal diarrhea is one of the most severe diseases in human beings and pigs, leading to high mortality and growth faltering. Gut microbiome-related studies mostly focus on the relationship between bacteria and neonatal diarrhea onset, and no research study has investigated the role of the gut virome in neonatal diarrhea. Here, using metagenomic sequencing, we characterized the fecal viral community of diarrheal and healthy neonatal piglets. We found that the viral community of diarrheal piglets showed higher individual heterogeneity and elevated abundance of Myoviridae. By predicting the bacterial host of the identified viral genomes, phages infecting Proteobacteria, especially E. coli, were the dominant taxa in neonatal diarrheal piglets. Consistent with this, the antibiotic resistance gene of E. coli origin was also enriched in neonatal diarrheal piglets. Finally, we established a random forest model to accurately discriminate between neonatal diarrheal piglets and healthy controls and identified genus E. coli- and genus listeria-infecting bacteriophages, including psa and C5 viruses, as key biomarkers. In conclusion, we provide the first glance of viral community and function characteristics in diarrheal and healthy neonatal piglets. These findings expand our understanding of the relationship among phages, bacteria and diarrhea, and may facilitate the development of therapeutics for the prevention and treatment of neonatal diarrhea.

Viral Metagenomic Analysis of the Fecal Samples in Domestic Dogs (Canis lupus familiaris)

Canine diarrhea is a common intestinal illness that is usually caused by viruses, bacteria, and parasites, and canine diarrhea may induce morbidity and mortality of domestic dogs if treated improperly. Recently, viral metagenomics was applied to investigate the signatures of the enteric virome in mammals. In this research, the characteristics of the gut virome in healthy dogs and dogs with diarrhea were analyzed and compared using viral metagenomics. The alpha diversity analysis indicated that the richness and diversity of the gut virome in the dogs with diarrhea were much higher than the healthy dogs, while the beta diversity analysis revealed that the gut virome of the two groups was quite different. At the family level, the predominant viruses in the canine gut virome were certified to be Microviridae, Parvoviridae, Siphoviridae, Inoviridae, Podoviridae, Myoviridae, and others. At the genus level, the predominant viruses in the canine gut virome were certified to be Protoparvovirus, Inovirus, Chlamydiamicrovirus, Lambdavirus, Dependoparvovirus, Lightbulbvirus, Kostyavirus, Punavirus, Lederbergvirus, Fibrovirus, Peduovirus, and others. However, the viral communities between the two groups differed significantly. The unique viral taxa identified in the healthy dogs group were Chlamydiamicrovirus and Lightbulbvirus, while the unique viral taxa identified in the dogs with diarrhea group were Inovirus, Protoparvovirus, Lambdavirus, Dependoparvovirus, Kostyavirus, Punavirus, and other viruses. Phylogenetic analysis based on the near-complete genome sequences showed that the CPV strains collected in this study together with other CPV Chinese isolates clustered into a separate branch, while the identified CAV-2 strain D5-8081 and AAV-5 strain AAV-D5 were both the first near-complete genome sequences in China. Moreover, the predicted bacterial hosts of phages were certified to be Campylobacter, Escherichia, Salmonella, Pseudomonas, Acinetobacter, Moraxella, Mediterraneibacter, and other commensal microbiota. In conclusion, the enteric virome of the healthy dogs group and the dogs with diarrhea group was investigated and compared using viral metagenomics, and the viral communities might influence canine health and disease by interacting with the commensal gut microbiome.