Altered Gut Microbiota Profiles in Sows and Neonatal Piglets Associated with Porcine Epidemic Diarrhea Virus Infection

Probiotic Bacillus licheniformis DSMZ 28710 improves sow milk microbiota and enhances piglet health outcomes

Maintaining a diverse and balanced sow milk microbiome is essential to piglet development. Thus, this study aimed to examine the effects of probiotic Bacillus licheniformis supplementation on the microbiome composition of sow colostrum and milk, and to review associated health findings in piglets. B. licheniformis DSMZ 28710 was supplemented at 10 g/day as feed additive before predicted farrowing until weaning by top dressing. Colostrum and milk samples were collected for metagenomic DNA extraction, 16s rRNA sequencing, and bioinformatics analyses for bacterial microbiota diversity. Results indicated that the supplementation increased the abundances of beneficial bacteria, such as Lactobacillus, Pediococcus, Bacteroides, and Bifidobacterium, while decreasing the abundances of pathogenic bacteria, such as Staphylococcus aureus, Enterobacteriaceae, and Campylobacter in the colostrum. The supplementation increased diversity while maintaining richness and evenness. Moreover, the rise in predicted microbial community metabolic function in membrane transport pathways provides crucial evidence showing that the supplementation is potentially beneficial to piglets, as these pathways are important for providing nutrients and immunity to offspring. This research highlights the importance of microbiome composition in sow milk and the potential of B. licheniformis supplementation as a means to improve piglet health and development.

Plant-Derived Polysaccharides Benefit Weaned Piglets by Regulating Intestinal Microbiota: A Review

The intestine harbors a community of bacteria that is intestinal microbiota, which is a complex and highly diverse community. This review discusses the gut microbiota in piglets, including the role of intestinal homeostasis in maintaining piglet health and the various factors that influence gut microbiota. Nutritional interventions, particularly the supplementation of plant-derived polysaccharides, including dietary fiber, for weaned piglets have been shown to enhance the abundance and colonization of beneficial intestinal microbes, reduce the incidence of gastrointestinal infections, and decrease the frequency of diarrhea, thereby improving gut health and growth performance. In this context, various polysaccharides, such as those derived from Medicago sativa L. (alfalfa), Glycyrrhiza uralensis Fisch. (licorice), and Lycium barbarum L. (wolfberry), Panax ginseng C.A. Mey. (ginseng), and Astragalus membranaceus (Fisch.) Bunge (astragalus) has demonstrated significant success. Additionally, dietary fibers such as inulin, pectin, beta-glucans, gums, cellulose, resistant starch, and starch derivatives have shown potential in regulating the gastrointestinal microbiota. Research has also explored the correlation between the structural characteristics of dietary polysaccharides and their biological activities. This review will pave the way for the development and utilization of plant-derived polysaccharides as effective non-antibiotic alternatives to restore gut microbial balance in weaning piglets.

Comparative analysis of fecal microbiota between diarrhea and non-diarrhea piglets reveals biomarkers of gut microbiota associated with diarrhea

Diarrhea poses a significant threat to the health and well-being of weaned piglets, leading to substantial morbidity and mortality and economic loss in the pig industry. However, the structural characteristics of the gut microbiota and the key genera associated with early diarrhea in piglets within large-scale production systems are poorly understood. This study aimed to investigate the differences in the microbial community structure and the specific genera alteration between the healthy piglets and diarrhea piglets, and to identify the biomarkers of gut microbiota associated with diarrhea in piglets. A total of 250 fecal samples, including 130 healthy piglets (Duroc × Landrace × Large Yorkshire) in the Control group and 120 from diarrhea piglets in Diarrhea group, were collected from three large-scale farms as discovery cohorts and were used for 16S rRNA gene sequencing. Additionally, 150 fecal samples from another large-scale pig farm were collected for the validation trail. The Chao1 and ACE indices were obviously lower (P < 0.01) in the diarrhea piglets compared to the healthy ones. Principal coordinate analysis showed significant differences in the distance matrix of gut microbiota between the healthy and diarrhea piglets (Bray-Curtis: P = 0.001, Jaccard: P = 0.001). Eighty-five genera were differentially enriched (P < 0.001) between healthy and diarrhea piglets. Notably, Treponema, Sphaerochaeta, Escherichia-Shigella, Slackia, and Staphylococcus were identified as potential biomarkers of diarrhea susceptibility; Clostridium sensu stricto 1, Prevotella_9, Olsenella, Dorea, and Lachnospiraceae NK4A136 group were found to be beneficial for maintaining intestinal homeostasis. These differentially enriched genera of healthy and diarrhea piglets were further confirmed in the validation cohort. In conclusion, this study identified the diarrhea-associated and beneficial genera in the faces of piglet, providing a theoretical basis for the diagnosis and intervention of diarrhea in weaned piglets.

Targeting gut-microbiota for gastric cancer treatment: a systematic review

Background

Preclinical research has identified the mechanisms via which bacteria influence cancer treatment outcomes. Clinical studies have demonstrated the potential to modify the microbiome in cancer treatment. Herein, we systematically analyze how gut microorganisms interact with chemotherapy and immune checkpoint inhibitors, specifically focusing on how gut bacteria affect the pharmacokinetics and pharmacodynamics of cancer treatment.

Method

This study searched Web of Science, Scopus, and PubMed until August 2023. Studies were screened by their title and abstract using the Rayyan intelligent tool for systematic reviews. Quality assessment of studies was done using the JBI critical appraisal tool.

Result

Alterations in the gut microbiome are associated with gastric cancer and precancerous lesions. These alterations include reduced microbial alpha diversity, increased bacterial overgrowth, and decreased richness and evenness of gastric bacteria. Helicobacter pylori infection is associated with reduced richness and evenness of gastric bacteria, while eradication only partially restores microbial diversity. The gut microbiome also affects the response to cancer treatments, with higher abundances of Lactobacillus associated with better response to anti-PD-1/PD-L1 immunotherapy and more prolonged progression-free survival. Antibiotic-induced gut microbiota dysbiosis can reduce the anti-tumor efficacy of 5-Fluorouracil treatment, while probiotics did not significantly enhance it. A probiotic combination containing Bifidobacterium infantis, Lactobacillus acidophilus, Enterococcus faecalis, and Bacillus cereus can reduce inflammation, enhance immunity, and restore a healthier gut microbial balance in gastric cancer patients after partial gastrectomy.

Conclusion

Probiotics and targeted interventions to modulate the gut microbiome have shown promising results in cancer prevention and treatment efficacy.Systematic review registration: https://osf.io/6vcjp.

Swine Colibacillosis: Analysis of the Gut Bacterial Microbiome

This study aimed to evaluate the disruption of the swine gut microbiota and histopathological changes caused by infection with enterotoxigenic E. coli. Fecal samples were collected from piglets suffering from diarrhea post-recovery and healthy animals. Intestinal tissues were collected for histopathological changes. The results revealed histopathological changes mainly in the ileum of the infected animals compared to those in the ileum of the control and recovered animals. The operational taxonomic units (OTUs) revealed that the E. coli diarrheal group exhibited the highest bacterial richness. Principal coordinate analysis (PCoA) corroborated the presence of dysbiosis in the gut microbiota following E. coli-induced diarrhea. While the normal control and infected groups displayed slight clustering, the recovery group formed a distinct cluster with a distinct flora. Bacteroidetes, Firmicutes, and Fusobacteria were the dominant phyla in both the healthy and recovered piglets and in the diarrheal group. LEfSe and the associated LDA score analysis revealed that the recovered group exhibited dominance of the phyla Euryarchaeota and Bacteroidota, while groups N and I showed dominance of the phyla Firmicutes and Fusobacteriota, respectively. The LDA scores highlighted a significant expression of the Muribaculacea family in group R. The obtained findings will help in understanding the microbiome during swine colibacillosis, which will support control of the outbreaks.

Gut microbiota-derived butyrate promotes coronavirus TGEV infection through impairing RIG-I-triggered local type I interferon responses via class I HDAC inhibition

Gut microbiota-derived metabolites are important for the replication and pathogenesis of many viruses. However, the roles of bacterial metabolites in swine enteric coronavirus (SECoV) infection remain poorly understood. Recent studies show that SECoVs infection in vivo significantly alters the composition of short-chain fatty acids (SCFAs)-producing gut microbiota. This prompted us to investigate whether and how SCFAs impact SECoV infection. Employing alphacoronavirus transmissible gastroenteritis virus (TGEV), a major cause of diarrhea in piglets, as a model, we found that SCFAs, particularly butyrate, enhanced TGEV infection both in porcine intestinal epithelial cells and swine testicular (ST) cells at the late stage of viral infection. This effect depended on the inhibited productions of virus-induced type I interferon (IFN) and downstream antiviral IFN-stimulated genes (ISGs) by butyrate. Mechanistically, butyrate suppressed the expression of retinoic acid-inducible gene I (RIG-I), a key viral RNA sensor, and downstream mitochondrial antiviral-signaling (MAVS) aggregation, thereby impairing type I IFN responses and increasing TGEV replication. Using pharmacological and genetic approaches, we showed that butyrate inhibited RIG-I-induced type I IFN signaling by suppressing class I histone deacetylase (HDAC). In summary, we identified a novel mechanism where butyrate enhances TGEV infection by suppressing RIG-I-mediated type I IFN responses. Our findings highlight that gut microbiota-derived metabolites like butyrate can be exploited by SECoV to dampen innate antiviral immunity and establish infection in the intestine.IMPORTANCESwine enteric coronaviruses (SECoVs) infection in vivo alters the composition of short-chain fatty acids (SCFAs)-producing gut microbiota, but whether microbiota-derived SCFAs impact coronavirus gastrointestinal infection is largely unknown. Here, we demonstrated that SCFAs, particularly butyrate, substantially increased alphacoronavirus TGEV infection at the late stage of infection, without affecting viral attachment or internalization. Furthermore, enhancement of TGEV by butyrate depended on impeding virus-induced type I interferon (IFN) responses. Mechanistically, butyrate suppressed the cytoplasmic viral RNA sensor RIG-I expression and downstream type I IFN signaling activation by inhibiting class I HDAC, thereby promoting TGEV infection. Our work reveals novel functions of gut microbiota-derived SCFAs in enhancing enteric coronavirus infection by impairing RIG-I-dependent type I IFN responses. This implies that bacterial metabolites could be therapeutic targets against SECoV infection by modulating antiviral immunity in the intestine.

Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets

BACKGROUND

The gut microbiota is a critical factor in the regulation of host health, but the relationship between the differential resistance of hosts to pathogens and the interaction of gut microbes is not yet clear. Herein, we investigated the potential correlation between the gut microbiota of piglets and their disease resistance using single-cell transcriptomics, 16S amplicon sequencing, metagenomics, and untargeted metabolomics.

RESULTS

Porcine epidemic diarrhea virus (PEDV) infection leads to significant changes in the gut microbiota of piglets. Notably, Landrace pigs lose their resistance quickly after being infected with PEDV, but transplanting the fecal microbiota of Min pigs to Landrace pigs alleviated the infection status. Macrogenomic and animal protection models identified Lactobacillus reuteri and Lactobacillus amylovorus in the gut microbiota as playing an anti-infective role. Moreover, metabolomic screening of the secondary bile acids' deoxycholic acid (DCA) and lithocholic acid (LCA) correlated significantly with Lactobacillus reuteri and Lactobacillus amylovorus, but only LCA exerted a protective function in the animal model. In addition, LCA supplementation altered the distribution of intestinal T-cell populations and resulted in significantly enriched CD8+ CTLs, and in vivo and in vitro experiments showed that LCA increased SLA-I expression in porcine intestinal epithelial cells via FXR receptors, thereby recruiting CD8+ CTLs to exert antiviral effects.

CONCLUSIONS

Overall, our findings indicate that the diversity of gut microbiota influences the development of the disease, and manipulating Lactobacillus reuteri and Lactobacillus amylovorus, as well as LCA, represents a promising strategy to improve PEDV infection in piglets. Video Abstract.

Mini-review: microbiota have potential to prevent PEDV infection by improved intestinal barrier

Porcine epidemic diarrhea virus (PEDV) infection poses a significant threat to the global pig industry. Current prevention and control strategies are inadequate in protecting pigs from new PEDV variants. This review aims to examine the relationship between PEDV and intestinal microbes, and investigate whether modulating intestinal microbes could affect PEDV infection. The mechanisms by which various intestinal microbes affect viral infection were initially introduced. Intestinal microbes can influence enteric viral infection through direct contact, such as binding, or by affecting interferons (IFNs) production and the intestinal barrier. Influencing the intestinal barrier by microbes can impact PEDV infection in young piglets. To narrow down the range of microbes that may influence PEDV infection, this review summarized microbes that change after infection. Short chain fatty acids (SCFAs), bacterial cell components, and toxins from microbes were identified as important mediators affecting PEDV infection. SCFAs primarily strengthen the intestinal barrier and inhibit intestinal inflammation, while bacterial cell components and toxins are more likely to damage the intestinal barrier. Therefore, this review hypothesizes that fecal transplantation, which allows the host to colonize more SCFAs-producing microbes, may prevent PEDV infection. However, these hypotheses require further proof, and the transplantation of intestinal microbes in pigs requires more exploration.

Hypericum japonicum extract inhibited porcine epidemic diarrhea virus in vitro and in vivo

Porcine epidemic diarrhea virus (PEDV) infection causes lethal watery diarrhea and high mortality in neonatal piglets, leading to huge economic losses in the global swine industry. Currently, the existing commercial vaccines cannot fully control PEDV, so it is urgent to develop effective antiviral agents to complement vaccine therapy. In the present study, we investigated the antiviral effect of Hypericum japonicum extract (HJ) against PEDV in vivo and in vitro. In in vitro assays, HJ could directly inactivate PEDV strains; moreover, it inhibited the proliferation of PEDV strains in Vero or IPI-FX cells at its non-cytotoxic concentrations. Time of addition assays revealed that HJ mainly inhibited PEDV at the later stages of the viral life cycle. In in vivo, compared with the model group, HJ could reduce the viral titers in the intestines of infected piglets, and improve their intestinal pathological, indicating that HJ could protect the newborn piglets from highly pathogenic PEDV variant infection. Furthermore, this effect may be related to the fact that HJ can not only directly inhibit viruses, but also regulate the structure of intestinal microbiota. In conclusion, our results indicate that Hypericum japonicum could inhibit PEDV replication in vitro and in vivo and might possess the potential to develop as the anti-PEDV drug.

Improving adsorption effect of modified carbon felt on microorganisms in pig houses

The pathogenic microorganisms in the air have a significant impact on piglet growth and even biosecurity of pig industry. Carbon felt-based microbial adsorption shows great potential in reducing the misuse of chemical disinfectants in pig houses. However, poor biocompatibility and low adsorption efficiency hinder the application of carbon felt for microbial control in animal husbandry. Herein, modified carbon felt was prepared with strong acid to improve its surface properties and internal structure. The hydrophilic and large specific surface area of modified sample offered high adsorption activity for bacteria adhered on biotic/abiotic interface. Fourier transform infrared spectrometer, X-ray diffraction, pore specific surface area analysis, and scanning electron microscopy were used to analyze the chemical functional groups and microporous structure of the modified carbon felt. Antibacterial tests were performed using the model bacteria Escherichia coli. Acid treatment converts the hydrophobicity of carbon felt to hydrophilicity, increasing adsorption capacity and promoting a disinfection rate of up to 97.3%. This study can enhance bioaffinity and adsorption selectivity of carbon felt to Escherichia coli, bringing its antibacterial activity and application prospects closer to industrialization.

Co-infection of porcine deltacoronavirus and porcine epidemic diarrhoea virus alters gut microbiota diversity and composition in the colon of piglets

Porcine deltacoronavirus (PDCoV) and porcine epidemic diarrhoea virus (PEDV) are the main porcine enteric coronaviruses that cause severe diarrhoea in piglets, posing huge threat to the swine industry. Our previous study verified that the co-infection of PDCoV and PEDV is common in natural swine infections and obviously enhances the disease severity in piglets. However, the effects of co-infection of PDCoV and PEDV on intestinal microbial community are unknown. In current study, the microbial composition and diversity in the colon of piglets were analyzed. Our results showed that both of PDCoV and PEDV were mainly distributed in the small intestines and caused severe damage of ileum but not colon in the co-inoculated piglets. Furthermore, we observed that PDCoV and PEDV co-infection alters the gut microbiota composition at the phylum, family and genus levels. The abundance of Mitsuokella and Collinsella at genus level were significantly increased in PDCoV-PEDV co-infection piglets. Spearman's correlation analysis further suggested that there existed strong positive correlation between Mitsuokella and TNF-α, IL-6 and IL-8 secretion, these two factors may together aggravating the small intestine pathological lesions. These results proved there existed obvious correlation between the disease severity caused by PDCoV-PEDV co-infection and intestinal microbial community.

Transcription Analysis of Liver and Muscle Tissues from Landrace Finishing Pigs with Different Feed Conversion Ratios

The efficiency of feed utilization determines the cost and economic benefits of pig production. In the present study, two pairs of full-sibling and two pairs of half-sibling female Landrace finishing pigs were selected, with each pair including individuals with different feed conversion rates, with liver and longissimus muscle tissue samples collected from each group for transcriptome analysis. A total of 561 differentially expressed genes (DEGs), among which 224 were up-regulated and 337 were down-regulated, were detected in the liver transcriptomes in the high-feed efficiency group compared to the low-feed efficiency group. The DEGs related to phosphorus and phosphate metabolism, arginine biosynthesis, chemical carcinogenesis, cytokine-cytokine receptor interaction, the biosynthesis of amino acids, and drug metabolism-cytochrome P450 in liver tissue were also associated with feed efficiency. In total, 215 DEGs were screened in the longissimus muscle tissue and were mainly related to disease and immune regulation, including complement and coagulation cascades, systemic lupus erythematosus, and prion diseases. The combination of gene expression and functional annotation results led to the identification of candidate feed efficiency-related biomarkers, such as ARG1, ARG2, GOT1, GPT2, ACAA2, ACADM, and ANGPTL4, members of cytochrome P450 family, and complement component family genes. Although the novel feed efficiency-related candidate genes need to be further evaluated by a larger sample size and functional studies, the present study identifies novel candidate biomarkers for the identification of functional SNPs underlying porcine feed efficiency.

Difference analysis of intestinal microbiota and metabolites in piglets of different breeds exposed to porcine epidemic diarrhea virus infection

The gut microbial composition of the Luchuan (LC) piglet, one of China’s native breeds, has rarely been studied, especially when compared to other breeds. This study developed a porcine epidemic diarrhea virus (PEDV) infection model in LC and Largewhite (LW) piglets, and analyzed the patterns and differences of intestinal microbial communities and metabolites in piglets of these two breeds after infection. The diarrhea score, survival time, and distribution of viral antigens in the intestine of piglets infected with PEDV differed among breeds, with the jejunal immunohistochemistry score of LW piglets being significantly higher than that of LC piglets (P < 0.001). The results of 16S rRNA sequencing showed differences in microbial diversity and community composition in the intestine of piglets with different breeds between PEDV infection piglets and the healthy controls. There were differences in the species and number of dominant phyla and dominant genera in the same intestinal segment. The relative abundance of Shigella in the jejunum of LC piglets after PEDV infection was significantly lower than that of LW piglets (P < 0.05). The key microorganisms differed in the microbiota were Streptococcus alactolyticus, Roseburia faecis, Lactobacillus iners, Streptococcus equi, and Lactobacillus mucosae (P < 0.05). The non-targeted metabolite analysis revealed that intestinal metabolites showed great differences among the different breeds related to infection. Spearman correlation analysis was conducted to examine any links between the microbiota and metabolites. The metabolites in the intestine of different breeds related to infection were mainly involved in arginine biosynthesis, synaptic vesicle cycle, nicotinic acid and nicotinamide metabolism and mTOR signaling pathway, with significantly positive or negative correlations (P < 0.05) between the various microorganisms. This study provides a theoretical foundation for investigating the application of core microorganisms in the gut of piglets of different breeds in the digestive tracts of those infected with PEDV, and helps to tackle the antimicrobial resistance problem further.

Rotavirus Infection in Swine: Genotypic Diversity, Immune Responses, and Role of Gut Microbiome in Rotavirus Immunity

Rotaviruses (RVs) are endemic in swine populations, and all swine herds certainly have a history of RV infection and circulation. Rotavirus A (RVA) and C (RVC) are the most common among all RV species reported in swine. RVA was considered most prevalent and pathogenic in swine; however, RVC has been emerging as a significant cause of enteritis in newborn piglets. RV eradication from swine herds is not practically achievable, hence producers’ mainly focus on minimizing the production impact of RV infections by reducing mortality and diarrhea. Since no intra-uterine passage of immunoglobulins occur in swine during gestation, newborn piglets are highly susceptible to RV infection at birth. Boosting lactogenic immunity in gilts by using vaccines and natural planned exposure (NPE) is currently the only way to prevent RV infections in piglets. RVs are highly diverse and multiple RV species have been reported from swine, which also contributes to the difficulties in preventing RV diarrhea in swine herds. Human RV-gut microbiome studies support a link between microbiome composition and oral RV immunogenicity. Such information is completely lacking for RVs in swine. It is not known how RV infection affects the functionality or structure of gut microbiome in swine. In this review, we provide a detailed overview of genotypic diversity of swine RVs, host-ranges, innate and adaptive immune responses to RVs, homotypic and heterotypic immunity to RVs, current methods used for RV management in swine herds, role of maternal immunity in piglet protection, and prospects of investigating swine gut microbiota in providing immunity against rotaviruses.

Enterotoxigenic Escherichia coli infection of weaned pigs: Intestinal challenges and nutritional intervention to enhance disease resistance

Enterotoxigenic Escherichia coli (ETEC) infection induced post-weaning diarrhea is one of the leading causes of morbidity and mortality in newly weaned pigs and one of the significant drivers for antimicrobial use in swine production. ETEC attachment to the small intestine initiates ETEC colonization and infection. The secretion of enterotoxins further disrupts intestinal barrier function and induces intestinal inflammation in weaned pigs. ETEC infection can also aggravate the intestinal microbiota dysbiosis due to weaning stress and increase the susceptibility of weaned pigs to other enteric infectious diseases, which may result in diarrhea or sudden death. Therefore, the amount of antimicrobial drugs for medical treatment purposes in major food-producing animal species is still significant. The alternative practices that may help reduce the reliance on such antimicrobial drugs and address animal health requirements are needed. Nutritional intervention in order to enhance intestinal health and the overall performance of weaned pigs is one of the most powerful practices in the antibiotic-free production system. This review summarizes the utilization of several categories of feed additives or supplements, such as direct-fed microbials, prebiotics, phytochemicals, lysozyme, and micro minerals in newly weaned pigs. The current understanding of these candidates on intestinal health and disease resistance of pigs under ETEC infection are particularly discussed, which may inspire more research on the development of alternative practices to support food-producing animals.

In vivo assessment of bacteriophages specific to multidrug resistant Escherichia coli on fecal bacterial counts and microbiome in nursery pigs

Escherichia coli is the most common cause of economic loss in swine industry. Nowadays, bacteriophages have been proven as good candidates for controlling bacterial infections. In this study, 6 phages were isolated and selected based on their high efficacy against 11 stains of E. coli isolated from diarrheal pigs. Six groups of weaned piglets were assigned (control, bacterial control (BC), two phage control (PC) and two phage treatment (PT) groups). Two titers (2 × 10⁹ PFU/animal and 2 × 10¹⁰ PFU/animal) of phage cocktails consisting of these phages were tested in the PC and PT groups via oral gavage at 24, 48, and 72 h against an E. coli cocktail (2 × 10⁹ CFU/animal) that was given to the piglets at 0, 12, 24, and 48 h of the trial. A significant reduction of fecal E. coli counts was observed in both PT groups from day 1 to 7 following the final phage dosage when compared to those of the BC group. Microbiomes in feces obtained 24 h after the final phage administration revealed phage therapy with both dosages could restore the gut's bacterial composition. Moreover, the given phage cocktails resulted in a significantly higher average daily gain of piglets during the first few weeks in both PC groups and the PT group receiving a higher phage dosage. These findings suggest that bacteriophages might be a potential alternative to antibiotics in the treatment of pathogens. In addition, they could also be utilized to improve pig growth performance.

The sow microbiome: Current and future perspectives to maximize the productivity in swine herds

The development of new generation sequencing methods and the reduction in the cost per base sequenced over the past few years is drawing the attention of the pig industry to microbiome understanding and modulation. In recent years, there has been an increase in the number of articles published related to microbiome studies in swine. With respect to sows, microbiome studies mainly focused on the gut, with some studies evaluating the reproductive tract and mammary microbiome. However, studies about urinary microbiome are still lacking. The present literature indicates that the microbiome in the sow’s gut can affect the microbiome in other body parts. Moreover, the understanding of the dynamics and interactions among microbial populations within the sow or the herd has led to improvements in animal health and reproductive performance. This review provides new insights related to sow intestinal, urinary, mammary, and reproductive microbiomes and their relationships with reproductive outcomes, diseases, and early colonization in offspring by gathering the most recent work in this field as well as pinpoints information gaps that require further investigation. This literature review also sheds light on the knowledge regarding the role of microbiomes in the reduction of antimicrobial use.

Biological units of antimicrobial resistance and strategies for their containment in animal production

The increasing prevalence of antimicrobial resistant bacterial infections has ushered in a major global public health crisis. Judicious or restricted antimicrobial use in animal agriculture, aiming to confine the use for the treatment of infections, is the most commonly proposed solution to reduce selection pressure for resistant bacterial strains and resistance genes. However, a multifaceted solution will likely be required to make acceptable progress in reducing antimicrobial resistance, due to other common environmental conditions maintaining antimicrobial resistance and limited executionary potential as human healthcare and agriculture will continue to rely heavily on antimicrobials in the foreseeable future. Drawing parallels from systematic approaches to the management of infectious disease agents and biodiversity loss, we provide examples that a more comprehensive approach is required, targeting antimicrobial resistance in agroecosystems on multiple fronts simultaneously. We present one such framework, based on nested biological units of antimicrobial resistance, and describe established or innovative strategies targeting units. Some of the proposed strategies are already in use or ready to be implemented, while some require further research and discussion among scientists and policymakers. We envision that antimicrobial resistance mitigation strategies for animal agriculture combining multiple tools would constitute powerful ecosystem-level interventions necessary to mitigate antimicrobial resistance.

Alterations of Suckling Piglet Jejunal Microbiota Due to Infection With Porcine Epidemic Diarrhea Virus and Protection Against Infection by Lactobacillus salivarius

The high mortality of neonatal piglets due to porcine epidemic diarrhea virus (PEDV) infection has caused huge economic losses to the pig industry. The intestinal microbiota is an important barrier against invaders entering the gastrointestinal route. In this study, we examined the differences between intestinal microbiota of PEDV-infected and healthy piglets. According to the viral copy numbers, 16 crossbred (Landrace-Yorkshire) piglets were divided into three groups: uninfected, low virus load, and high virus load groups. Next, 16S rRNA sequencing was performed to determine the microbiota composition in jejunal content and jejunal mucosal samples from the three groups. PEDV infection induced an imbalance in the microbiota of both jejunal content and jejunal mucosa. The abundance of phylum Firmicutes was higher in uninfected piglets than in infected piglets, whereas the abundance of Proteobacteria was lower in uninfected piglets. Principal coordinate analysis showed significant separation of jejunal microbiota between different groups. Linear discriminant analysis (LDA) effect size (LEfSe) identified Lactobacillus salivarius as a potential biomarker among three groups at the level of species. Then, in vitro, L. salivarius was able to suppress the infection of PEDV to IPEC-J2 cells and decreased the expression of GRP78 (Glucose-regulating protein 78). In addition, we detected the mRNA expression of genes involved in the FAK/PI3K/Akt signaling pathway. When IPEC-J2 cells were treated with L. salivarius before PEDV infection, the mRNA expression levels of ITGA1, ITGA5, ITGB5, FAK, PIK3R1, PIK3CA and AKT1 were significantly higher than those in the control cells (without treatment) at different times post-infection, indicating that L. salivarius may upregulate the FAK/PI3K/Akt signaling pathway in IPEC-J2 cells to resist PEDV infection. In summary, PEDV infection altered microbial communities in both jejunal content and jejunal mucosa. L. salivarius has a protective effect against PEDV infection in IPEC-J2 cells. This study provides a potentially effective strategy to prevent the occurrence and control the spread of PED in the pig production.

Effects of probiotic supplements on growth performance and intestinal microbiota of partridge shank broiler chicks

Background

The benefits of probiotics being used in animals are well-documented via evidenced growth performance improvement and positive modulations of gut microbiota (GM). Thus, a combination of effective microorganisms (EM) has been frequently used in animal production, including broilers. However, there are only very limited reports of EM on the growth performance and the modulation in GM of partridge shank broiler chicks.

Methods

We attempted to evaluate the effects of a basal diet with the addition of an EM mixture on the growth performance and gut microbiome of the chicks. A total of 100 ten-day-old female partridge shank broiler chicks were randomly divided into two groups of 50 chicks each, of which, one group fed with EM supplementation in the basal diet (designated as EM-treated group), the other group just fed with a basal diet (referred as to non-EM treated group or control group). The body weight, daily feed intake, daily gain, feed conversion ratio and other growth parameters were observed and compared between EM-treated and non-EM-treated chicks, and the gut microbiota was profiled by 16S rRNA-based next generation sequencing (NGS).

Results

EM-treated chicks showed significantly increased performances in body weight (BW), average daily gain (ADG) and reduced feed conversion ratio (FCR). Histological observation indicated that dietary supplementation of EM significantly increased the villus heights (VH) and the ratio of villus height to crypt depth (VH/CD), while decreased the CD of jejunum, ilea, and ceca. The results of 16S rRNA-based gut microbiota analyses showed that Firmicutes accounted for the most of the relative abundance (63.24%∼92.63%), followed by Proteobacteria (0.62%∼23.94%), Bacteroidetes (0.80%∼7.85%), Actinobacteria (0.06%∼13.69%) and others in both EM-treated and non-EM-treated broiler chicks. The addition of EM could not alter the alpha diversity of gut microbiota. Compared with the non-EM-treated chicks, the abundances of bad bacteria in the phyla of Firmicutes, Euryarchaeota, and Ruminococcus were dramatically decreased in that of EM-treated chicks, while the abundances of good bacteria in the phyla of Actinobacteria and WPS-2 were significantly increased.

Conclusions

The supplementation of EM in feed could improve the growth performance and positively influence the morphological characteristics of the intestine, and ameliorate the community and structure of the intestinal microbiota of partridge shank broiler chicks.

In-Feed Supplementation of Resin Acid-Enriched Composition Modulates Gut Microbiota, Improves Growth Performance, and Reduces Post-Weaning Diarrhea and Gut Inflammation in Piglets

The weaning process represents a delicate phase for piglets, and is often characterized by lower feed intake, lower weight gain, diarrhea, and ultimately increased mortality. We aimed to determine the effects of RAC supplementation in diets on improving piglet growth and vitality, reducing post-weaning diarrhea, and enhancing gut health. In a 2 × 2 × 2 factorial experiment, we selected forty sows and their piglets. Piglets were followed until seven weeks of age. There were no significant differences found between RAC treated and control piglets until weaning (p = 0.26). However, three weeks after weaning, RAC treated piglets had higher body weight and average daily growth (ADG) than the control piglets (p = 0.003). In addition, the piglets that received RAC after weaning, irrespective of mother or prior creep feed treatment, had lower post-weaning diarrhea (PWD) and fecal myeloperoxidase (MPO) level than control piglets. Gut microbiota analysis in post-weaning piglets revealed that RAC supplementation significantly increased Lachnospiraceae_unclassified, Blautia, Butyricicoccus, Gemmiger and Holdemanella, and decreased Bacteroidales_unclassified. Overall, RAC supplementation to piglets modulated post-weaning gut microbiota, improved growth performance after weaning, reduced post-weaning diarrhea and reduced fecal myeloperoxidase levels. We therefore consider RAC to be a potential natural feed supplement to prevent enteric infections and improve growth performance in weaning piglets.

Responses of Vaginal Microbiota to Dietary Supplementation with Lysozyme and its Relationship with Rectal Microbiota and Sow Performance from Late Gestation to Early Lactation

Simple Summary

The vaginal microbiota has a crucial role for the health of the sow and the newborn piglet. The purpose of this study was to investigate the effect of dietary supplementation with lysozyme in the vaginal microbiota and evaluate its relationship with the fecal microbiota of the rectum and the reproductive performance of the sow. The results suggest that, lysozyme supplementation changed vaginal microbiota composition at different taxonomic levels, the changed vaginal microbiota was associated with variations in fecal microbiota, and these changes correlated with some reproductive performance of the sow.

Abstract

This study was conducted to evaluate the effects of dietary lysozyme (LZM) supplementation on the vaginal microbiota, as well as the relationship between vaginal microbiota and the fecal microbiota of rectum and the reproductive performance of the sow. A total of 60 Yorkshire × Landrace sows (3–6 of parity) were arranged from day 85 of gestation to the end of lactation in a completely randomized design with three treatments (control diet, control diet + lysozyme 150 mg/kg, control diet + lysozyme 300 mg/kg). The results showed that sows fed with lysozyme increased serum interleukin-10 (IL-10, p < 0.05) on day 7 of lactation. The vaginal microbiota varied at different taxonomic levels with LZM supplementation by 16S rRNA gene sequencing. The most representative changes included a decrease in Tenericutes, Streptococcus, Bacillus and increase in Bacteroidetes, Actinobacteria, Enterococcus, and Lactobacillus (p < 0.05). There were 777 OTUs existing in both, vaginal and fecal microbiota. The addition of LZM also decreased the abundance of Tenericutes (p < 0.05) in the vagina and feces. The changes in the microbiota were correlated in some cases positively with the performance of the sow, for example, Bacillus in feces was positively correlated with the neonatal weight (p < 0.05). These results indicate that the addition of lysozyme to the diet of sow during perinatal period promote the change of vaginal bacterial community after farrowing. The variations in vaginal microbiota are also associated with the changes in the fecal microbiology of the rectum and the reproductive performance of the sow. Therefore, it is concluded that dietary supplementation with lysozyme in sows in late gestation stage until early lactation, is beneficial to establish vaginal microbiota that seems to promote maternal health and reproductive performance.

kernInt: A Kernel Framework for Integrating Supervised and Unsupervised Analyses in Spatio-Temporal Metagenomic Datasets

The advent of next-generation sequencing technologies allowed relative quantification of microbiome communities and their spatial and temporal variation. In recent years, supervised learning (i.e., prediction of a phenotype of interest) from taxonomic abundances has become increasingly common in the microbiome field. However, a gap exists between supervised and classical unsupervised analyses, based on computing ecological dissimilarities for visualization or clustering. Despite this, both approaches face common challenges, like the compositional nature of next-generation sequencing data or the integration of the spatial and temporal dimensions. Here we propose a kernel framework to place on a common ground the unsupervised and supervised microbiome analyses, including the retrieval of microbial signatures (taxa importances). We define two compositional kernels (Aitchison-RBF and compositional linear) and discuss how to transform non-compositional beta-dissimilarity measures into kernels. Spatial data is integrated with multiple kernel learning, while longitudinal data is evaluated by specific kernels. We illustrate our framework through a single point soil dataset, a human dataset with a spatial component, and a previously unpublished longitudinal dataset concerning pig production. The proposed framework and the case studies are freely available in the kernInt package at https://github.com/elies-ramon/kernInt.

Impact of N-Acetylcysteine on the Gut Microbiota in the Piglets Infected With Porcine Epidemic Diarrhea Virus

This study was to investigate the impact of N-acetylcysteine (NAC) on the gut microbiota in the healthy piglets and the piglets infected with porcine epidemic diarrhea virus (PEDV). Forty seven-day-old piglets were allocated into four groups: control group, NAC group (supplemented with 50 mg/kg body weight NAC), PEDV group (inoculated with 10^4.5 TCID₅₀ PEDV), and PEDV+NAC group (PEDV infection + NAC supplementation). The intestinal content was collected for DNA extraction and Illumina sequencing. The PEDV-infected piglets displayed distinct bacterial communities compared to the healthy piglets. PEDV infection decreased the abundance of Shigella and increased the abundance of Lactobacillus, Odoribacter, Anaerovibrio, Helicobacter, unclassified Lachnospiraceae, and Sutterella; affected several functions associated with metabolism, barrier, and immune. NAC supplementation decreased the abundance of unclassified Rikenellaceae and increased the abundance of Lactobacillus, Streptococcus, and Enterococcus in the healthy piglets, decreased the abundance of Oscillospira and Prevotella and increased the abundance of Lactobacillus in the PEDV-infected piglets; altered multiple functions involving in amino acid metabolism, cell signaling, cellular community, disease-related pathways, endocrine, and excretory system. In conclusion, PEDV infection caused severe dysbiosis of gut microbiome, whereas NAC supplementation played a positive role in regulating the gut microbiome during PEDV infection. Therefore, substances that can regulate gut microbiota could be ideal candidates to prevent or treat PEDV infection.

Dietary osteopontin-enriched algal protein as nutritional support in weaned pigs infected with F18-fimbriated enterotoxigenic Escherichia coli

This study investigated the effects of dietary osteopontin (OPN)-enriched algal protein on growth, immune status, and fecal fermentation profiles of weaned pigs challenged with a live infection of F18-fimbriated enterotoxigenic E. coli (ETEC). At 21 d of age, 54 pigs (5.95 ± 0.28 kg BW; blocked by BW) were allotted to 1 of 3 experimental groups combining dietary and health statuses. A control diet, containing 1% wild-type algal protein, was fed to both sham-inoculated (NC) and ETEC-inoculated (PC) pigs, while the test diet contained 1% OPN-enriched algal protein as fed only to ETEC-inoculated pigs (OA). All pigs received their assigned dietary treatment starting at study initiation to permit a 10-d acclimation period prior to inoculation. Growth performance, fecal dry matter, as well as hematological, histopathological, immune, and microbiota outcomes were analyzed by ANOVA, where treatment and time were considered as fixed effects and pig as a random effect; significance was accepted at P < 0.05. Overall, ETEC-inoculated pigs (PC and OA) exhibited decreased (P < 0.05) ADG and G:F, as well as increased (P < 0.05) peripheral blood helper T-cells and total leukocyte counts, compared with NC pigs during the postinoculation period. The OA treatment also elicited the highest (P < 0.05) concentrations of circulating tumor necrosis factor-α and volatile fatty acid concentrations in luminal contents at various postinoculation time-points, compared with other treatments. A principal coordinate analysis based on Unifrac weighted distances indicated that NC and OA groups had similar overall bacterial community structures, while PC pigs exhibited greater diversity, but infection status had no impact on α-diversity. Osteopontin-specific effects on microbial community structure included enrichment within Streptococcus and Blautia genera and decreased abundance of 12 other genera as compared with PC pigs. Overall, ETEC-infected pigs receiving 1% OPN-enriched algal protein exhibited changes immunity, inflammatory status, and colonic microbial community structure that may benefit weanling pigs experiencing F18 ETEC infection.

The lung-gut axis during viral respiratory infections: the impact of gut dysbiosis on secondary disease outcomes

Bacteria that colonize the human gastrointestinal tract are essential for good health. The gut microbiota has a critical role in pulmonary immunity and host's defense against viral respiratory infections. The gut microbiota's composition and function can be profoundly affected in many disease settings, including acute infections, and these changes can aggravate the severity of the disease. Here, we discuss mechanisms by which the gut microbiota arms the lung to control viral respiratory infections. We summarize the impact of viral respiratory infections on the gut microbiota and discuss the potential mechanisms leading to alterations of gut microbiota's composition and functions. We also discuss the effects of gut microbial imbalance on disease outcomes, including gastrointestinal disorders and secondary bacterial infections. Lastly, we discuss the potential role of the lung-gut axis in coronavirus disease 2019.

Acute porcine epidemic diarrhea virus infection reshapes the intestinal microbiota

The intestinal microbiota is crucial to intestinal homeostasis. Porcine epidemic diarrhea virus (PEDV) is high pathogenic to intestines, causing diarrhea, even death in piglets. To investigate the detailed relationship between PEDV infection and intestinal microbiota, the composition and distribution of intestinal microbiota from pigs were first analyzed using 16S rRNA sequencing technology. The results demonstrated that the composition and distribution of microbes in different intestinal segments were quite similar between 1-week-old and 2-week-old piglets but different from 4-week-old (weaned) piglets. Then piglets at different ages were inoculated with PEDV. The results showed that the 1-week-old piglets exhibited the most severe pathogenicity comparing to the other age groups. Further investigations indicated that Lactobacillus, Escherichia coli, and Lactococcus in the intestinal microbiota of piglets were significantly changed by PEDV infection. These results strengthen our understanding of viruses influencing intestinal microbes and remind us of the potential association between PEDV and intestinal microbes.

Modulation of Gut Microbiota, Short-Chain Fatty Acid Production, and Inflammatory Cytokine Expression in the Cecum of Porcine Deltacoronavirus-Infected Chicks

Porcine deltacoronavirus (PDCoV) is a novel swine enteropathogenic coronavirus that causes watery diarrhea and induces proinflammatory cytokine responses in piglets. Our previous research showed that the specific-pathogen-free (SPF) chicks exhibited mild diarrhea and low fecal viral shedding, along with cecum lesions after PDCoV infection. Disturbances in the homeostasis of the gut microbiota have been associated with various diseases. We aimed to explore the effects of PDCoV infection on chick gut microbiota, short-chain fatty acid (SCFAs) production, and inflammatory cytokine expression in chicks, and also to investigate the relationship between gut microbiota and SCFAs or inflammatory cytokine expression of the PDCoV-infected chicks. Results obtained using 16S rRNA sequencing showed that infection with PDCoV strain HNZK-02 significantly altered the composition of chick gut microbiota, with the reduced abundance of Eisenbergiella and Anaerotruncus genera at 5 days post-inoculation (dpi) (P < 0.05), and an increased abundance of Alistipes genus at 17 dpi (P < 0.05). The production of SCFAs in the cecum of PDCoV HNZK-02–infected chicks, including acetic acid, propionic acid, and butyric acid, decreased in all cases. The expression of inflammatory cytokines (interferon-γ, tumor necrosis factor-α, and interleukin-10) was increased in the cecum tissue and serum of the PDCoV HNZK-02–infected chicks when detected by quantitative real-time polymerase chain reaction and enzyme-linked immunosorbent assay, respectively. Further analysis showed significant correlation between bacterial genera and SCFAs or inflammatory cytokines expression in cecum of the PDCoV infected chicks. These findings might provide new insight into the pathology and physiology of PDCoV in chicks.

Porcine epidemic diarrhea virus (PEDV): An update on etiology, transmission, pathogenesis, and prevention and control

Porcine epidemic diarrhea virus (PEDV), a member of the genus Alphacoronavirus in the family Coronaviridae, causes acute diarrhea and/or vomiting, dehydration and high mortality in neonatal piglets. Two different genogroups of PEDV, S INDEL [PEDV variant containing multiple deletions and insertions in the S1 subunit of the spike (S) protein, G1b] and non-S INDEL (G2b) strains were detected during the diarrheal disease outbreak in US swine in 2013-2014. Similar viruses are also circulating globally. Continuous improvement and update of biosecurity and vaccine strains and protocols are still needed to control and prevent PEDV infections worldwide. Although the non-S INDEL PEDV was highly virulent and the S INDEL PEDV caused milder disease, the latter has the capacity to cause illness in a high number of piglets on farms with low biosecurity and herd immunity. The main PEDV transmission route is fecal-oral, but airborne transmission via the fecal-nasal route may play a role in pig-to-pig and farm-to-farm spread. PEDV infection of neonatal pigs causes fecal virus shedding (alongside frequent detection of PEDV RNA in the nasal cavity), acute viremia, severe atrophic enteritis (mainly jejunum and ileum), and increased pro-inflammatory and innate immune responses. PEDV-specific IgA effector and memory B cells in orally primed sows play a critical role in sow lactogenic immunity and passive protection of piglets. This review focuses on the etiology, transmission, pathogenesis, and prevention and control of PEDV infection.

Medium-chain fatty acids and monoglycerides as feed additives for pig production: towards gut health improvement and feed pathogen mitigation

Ongoing challenges in the swine industry, such as reduced access to antibiotics and virus outbreaks (e.g., porcine epidemic diarrhea virus, African swine fever virus), have prompted calls for innovative feed additives to support pig production. Medium-chain fatty acids (MCFAs) and monoglycerides have emerged as a potential option due to key molecular features and versatile functions, including inhibitory activity against viral and bacterial pathogens. In this review, we summarize recent studies examining the potential of MCFAs and monoglycerides as feed additives to improve pig gut health and to mitigate feed pathogens. The molecular properties and biological functions of MCFAs and monoglycerides are first introduced along with an overview of intervention needs at different stages of pig production. The latest progress in testing MCFAs and monoglycerides as feed additives in pig diets is then presented, and their effects on a wide range of production issues, such as growth performance, pathogenic infections, and gut health, are covered. The utilization of MCFAs and monoglycerides together with other feed additives such as organic acids and probiotics is also described, along with advances in molecular encapsulation and delivery strategies. Finally, we discuss how MCFAs and monoglycerides demonstrate potential for feed pathogen mitigation to curb disease transmission. Looking forward, we envision that MCFAs and monoglycerides may become an important class of feed additives in pig production for gut health improvement and feed pathogen mitigation.

Porcine deltacoronavirus infection alters bacterial communities in the colon and feces of neonatal piglets

Porcine deltacoronavirus (PDCoV) is a novel enteropathogenic coronavirus that causes watery diarrhea in piglets. Little is known regarding the alteration of the gut microbiota in PDCoV‐induced diarrhea piglets. In this study, 5‐day‐old piglets were experimentally infected with PDCoV strain CH‐01, and all piglets developed typical clinical disease, characterized by acute and severe watery diarrhea. Histologic lesions were limited to the villous epithelium of the duodenum and ileum. Gut microbiota profiles in the colon and feces of piglets inoculated with PDCoV were investigated using 16S rRNA sequencing. The results showed that PDCoV infection reduced bacterial diversity and significantly altered the composition of the microbiota from the phylum to the genus level in the colon and feces of piglets. Firmicutes (phylum), Lactobacillaceae (family), and Lactobacillus (genus) were significantly increased (p < .01), while the abundance of Bacteroidetes (phylum) was markedly reduced in the colon and feces of the PDCoV‐infected piglets (p < .01) when compared to those of the healthy piglets. Furthermore, microbial function prediction indicated that the changes in the intestinal flora also affected the nucleotide transport and metabolism, defense, translation, and transcription function of the intestinal microbiota. The current study provides new insight into the pathology and physiology of PDCoV.

Composition and functional diversity of fecal bacterial community of wild boar, commercial pig and domestic native pig as revealed by 16S rRNA gene sequencing

The bacterial community in mammalian gastrointestinal tract is abundant and complex. To date, little is known about the gut microbiota of wild boar. This study aimed to investigate the fecal bacterial diversity of wild boar and compare with commercial pig and domestic native pig. The diet composition showed that the diets of wild boar, commercial pig and domestic native pig were different from each other. More than 1,760,000 quality-filtered sequences were obtained, and the results revealed distinct compositions and diversity of fecal microbiota in three groups. PCoA and NMDS analyses showed that fecal bacterial communities of wild boar, commercial pig and domestic native pig formed distinctly different clusters. Although the three groups shared a large size of OTUs comprising a core microbiota community, a strong distinction existed at family and genus levels. Ruminococcaceae, Prevotellaceae and Christensenellaceae were more abundant in the feces of wild boar than in domestic native pig and commercial pig. At the genus level, the proportion of unidentified Christensenellaceae was remarkably higher in wild boar group, while commercial pig and domestic native pig group had a higher abundance of Streptococcus and Lactobacillus. Tax4Fun predictions of metagenome function showed statistically significant differences in the functions of fecal microbiota in three groups. There were more bacteria genes with amino acid metabolism, cell growth and death, cell motility, energy metabolism, immune system and environmental adaptation observed in wild boar feces, while commercial pig feces contained more bacteria genes with carbohydrate metabolism, drug resistance, aging, infectious diseases, lipid metabolism, endocrine and metabolic diseases. These results indicated that the fecal microbial ecosystem of the wild boar is significantly different from that of domestic native pig and commercial pig, suggesting that diet is an important factor leading to differences in bacterial abundance and diversity in feces.

Microbiota in viral infection and disease in humans and farm animals

The influence of the microbiota on viral infection susceptibility and disease outcome is undisputable although varies among viruses. The purpose of understanding the interactions between microbiota, virus, and host is to identify practical, effective, and safe approaches that target microbiota for the prevention and treatment of viral diseases in humans and animals, as currently there are few effective and reliable antiviral therapies available. The initial step for achieving this goal is to gather clinical evidences, focusing on the viral pathogens-from human and animal studies-that have already been shown to interact with microbiota. The subsequent step is to identify mechanisms, through experimental evidences, to support the development of translational applications that target microbiota. In this chapter, we review evidences of virus infections altering microbiota and of microbiota enhancing or suppressing infectivity, altering host susceptibility to certain viral diseases, and influencing vaccine immunogenicity in humans and farm animals.

Porcine Epidemic Diarrhea Altered Colonic Microbiota Communities in Suckling Piglets

Porcine epidemic diarrhea (PED) is a major gastrointestinal disease afflicting suckling pigs that causes huge industrial economic losses. In this study, we investigated microbiota from the colonic mucosa and content in healthy and PED piglets. High-throughput 16S rRNA gene sequencing was performed to identify inter-group differences. Firmicutes, Fusobacteria, Proteobacteria, and Bacteroidetes were the top four affected phyla. The proportion of Proteobacteria was higher in infected than in healthy piglets, and the opposite was observed for Bacteroidetes (more than four-fold higher in the healthy group). In the infected group, Fusobacterium accounted for 36.56% and 21.61% in the colonic mucosa and contents, respectively, while in the healthy group, they comprised 22.53% and 12.67%, respectively. The percentage of Lactobacillus in healthy colons (15.63%) was considerably higher than that in the disease group (<10%). In both the colonic mucosa and contents, functional enrichment differed significantly between healthy and diseased groups. Overall, infection with the PED virus increased the proportion of harmful bacteria and decreased the proportion of beneficial bacteria in the colons of piglets. Targeting intestinal microbiota could be a promising method for PED prevention, thus opening new avenues for future research.

Evaluation of antiviral activity of Bacillus licheniformis-fermented products against porcine epidemic diarrhea virus

Bacillus licheniformis (B. licheniformis) is commonly used as probiotic and its secondary metabolites are attractive anti-microbial candidate. In the present study, we aimed to evaluate the antiviral activity of crude extracts from B. licheniformis against porcine epidemic diarrhea virus (PEDV), a highly contagious enveloped porcine virus that has caused great economic loss in pigs. In vivo, PEDV-infected piglets supplemented with air-dried solid state fermentative cultivate containing B. licheniformis-fermented products (BLFP) showed milder clinical symptoms and decreased viral shedding. Importantly, no significant systemic pathological lesions and no reduction in average daily gain were noted in pigs supplemented with the BLFP, which suggests that it is safe for use in pigs. In vitro experiments revealed that while B. licheniformis crude extracts exhibited no toxicity in Vero cells, co-cultivation of B. licheniformis crude extracts with PEDV significantly reduced viral infection and replication. Summarized current results suggest that the B. licheniformis-fermented products could be a novel candidate food additive for reducing the impact of PED on the swine industry.

Manipulation of Intestinal Antiviral Innate Immunity and Immune Evasion Strategies of Porcine Epidemic Diarrhea Virus

Porcine epidemic diarrhea virus (PEDV) infection causes watery diarrhea, dehydration, and high mortality in neonatal pigs, due to its clinical pathogenesis of the intestinal mucosal barrier dysfunction. The host's innate immune system is the first line of defence upon virus invasion of the small intestinal epithelial cells. In turn, the virus has evolved to modulate the host's innate immunity during infection, resulting in pathogen virulence, survival, and the establishment of successful infection. In this review, we gather current knowledge concerning the interplay between PEDV and components of host innate immunity, focusing on the role of cytokines and interferons in intestinal antiviral innate immunity, and the mechanisms underlying the immune evasion strategies of PEDV invasion. Finally, we provide some perspectives on the potential prevention and treatment for PEDV infection.

Changes in cecal microbiota community of suckling piglets infected with porcine epidemic diarrhea virus

Diarrhea, caused by porcine epidemic diarrhea virus (PEDV), is a catastrophic gastrointestinal disease among suckling piglets, with high infectivity, morbidity, and mortality, causing huge economic losses to the pig industry. In the present study, we investigated the different microbiota from the cecal mucosa and cecal contents between healthy and PEDV-infected piglets. High-throughput 16S rRNA gene sequencing was performed to explore differences. The results revealed that microbial dysbiosis by PEDV infection occurred in the cecal mucosa and contents of suckling piglets at each microbial taxonomic level. The abundance of pathogenic bacteria associated with diseases, including diarrhea, was increased. The abundance of Fusobacterium was 26.71% and 33.91% in cecal mucosa and contents of PEDV-infected group, respectively, whereas that in the healthy groups was 17.85% and 9.88%. The proportion of Proteobacteria in the infected groups was relatively high (24.67% and 22.79%, respectively), whereas that in the healthy group was 13.13% and 11.34% in the cecal mucosa and contents, respectively. Additionally, the proportion of Bacteroidetes in the healthy group (29.89%, 37.32%) was approximately twice that of the PEDV-infected group (15.50%, 15.39%). “Nitrate reduction”, “Human pathogens diarrhea”, “Human pathogens gastroenteritis”, “Nitrite respiration”, and “Nitrite ammonification” were the enriched functional annotation terms in the PEDV-infected groups. Porcine epidemic diarrhea virus infection increased the proportion of harmful bacteria and decreased the proportion of beneficial bacteria in the cecal mucosa and contents of suckling piglets. Our findings suggest that determining the intestinal microbiota might provide a promising method to prevent PEDV and open a new avenue for future research.

Stage of Gestation at Porcine Epidemic Diarrhea Virus Infection of Pregnant Swine Impacts Maternal Immunity and Lactogenic Immune Protection of Neonatal Suckling Piglets

During pregnancy, the maternal immune response changes dramatically over the course of gestation. This has implications for generation of lactogenic immunity and subsequent protection in suckling neonates against enteric viral infections. For example, porcine epidemic diarrhea virus (PEDV) is an alphacoronavirus that causes acute diarrhea in neonatal piglets. Due to the high virulence of PEDV and the naïve, immature immune system of neonatal suckling piglets, passive lactogenic immunity to PEDV induced during pregnancy, via the gut-mammary gland (MG)-secretory IgA (sIgA) axis, is critical for piglet protection. However, the anti-PEDV immune response during pregnancy and stage of gestation required to optimally stimulate the gut-MG-sIgA axis is undefined. We hypothesize that there is a gestational window in which non-lethal PEDV infection of pregnant gilts influences maximum lymphocyte mucosal trafficking to the MG, resulting in optimal passive lactogenic protection in suckling piglets. To understand how the stages of gestation affect maternal immune responses to PEDV, three groups of gilts were orally infected with PEDV in the first, second or third trimester. Control (mock) gilts were inoculated with medium in the third trimester. To determine if lactogenic immunity correlated with protection, all piglets were PEDV-challenged at 3–5 days postpartum. PEDV infection of gilts at different stages of gestation significantly affected multiple maternal systemic immune parameters prepartum, including cytokines, B cells, PEDV antibodies (Abs), and PEDV antibody secreting cells (ASCs). Pregnant second trimester gilts had significantly higher levels of circulating PEDV IgA and IgG Abs and ASCs and PEDV virus neutralizing (VN) Abs post PEDV infection. Coinciding with the significantly higher PEDV Ab responses in second trimester gilts, the survival rate of their PEDV-challenged piglets was 100%, compared with 87.2, 55.9, and 5.7% for first, third, and mock litters, respectively. Additionally, piglet survival positively correlated with PEDV IgA Abs and ASCs and VN Abs in milk and PEDV IgA and IgG Abs in piglet serum. Our findings have implications for gestational timing of oral attenuated PEDV maternal vaccines, whereby PEDV intestinal infection in the second trimester optimally stimulated the gut-MG-sIgA axis resulting in 100% lactogenic immune protection in suckling piglets.

Dynamic Change of Gut Microbiota During Porcine Epidemic Diarrhea Virus Infection in Suckling Piglets

Porcine epidemic diarrhea (PED) is a disease that has a devastating effect on livestock. Currently, most studies are focused on comparing gut microbiota of healthy piglets and piglets with PED, resulting in gut microbial populations related to dynamic change in diarrheal piglets being poorly understood. The current study analyzed the characteristics of gut microbiota in porcine epidemic diarrhea virus (PEDV)-infected piglets during the suckling transition stage. Fresh fecal samples were collected from 1 to 3-week-old healthy piglets (n = 20) and PEDV infected piglets (n = 18) from the same swine farm. Total DNA was extracted from each sample and the V3-V4 hypervariable region of the 16S rRNA gene was amplified and sequenced using the Illumina MiSeq platform. Statistically significant differences were observed in bacterial diversity and richness between the healthy and diarrheal piglets. Principal coordinates analysis (PCoA) showed structural segregation between diseased and healthy groups, as well as among 3 different age groups. The abundance of Escherichia-Shigella, Enterococcus, Fusobacterium, and Veillonella increased due to dysbiosis induced by PEDV infection. Notably, there was a remarkable age-related increase in Fusobacterium and Veillonella in diarrheal piglets. Certain SCFA-producing bacteria, such as Ruminococcaceae_UCG-002, Butyricimonas, and Alistipes, were shared by all healthy piglets, but were not identified in various age groups of diarrheal piglets. In addition, significant differences were observed between clusters of orthologous groups (COG) functional categories of healthy and PEDV-infected piglets. Our findings demonstrated that PEDV infection caused severe perturbations in porcine gut microbiota. Therefore, regulating gut microbiota in an age-related manner may be a promising method for the prevention or treatment of PEDV.