Pig Gut Microbiome Research Articles

Effect of host breeds on gut microbiome and fecal metabolome in commercial pigs

BackgroundGut microbial composition and its metabolites are crucial for livestock production performance. Metabolite profiles from autopsied biospecimens provide vital information on the basic mechanisms that affect the overall health and production traits in livestock animals. However, the role of the host breed in the gut microbiome and fecal metabolome of commercial pigs remains unclear. In this work, differences in microbiota composition among three commercial pig breeds Duroc, Yorkshire, and Landrace were measured by 16S rRNA gene sequencing. Fecal metabolite compositions of the three pig breeds were detected using untargeted metabolomics.ResultsThere were significant differences in the gut microbiomes of the three species, indicating that host breed affects the diversity and structure of gut microbiota. Several breed-associated microorganisms were identified at different taxonomic levels. Notely, most microbial taxa were annotated as Lactobacillacea, Muribaculaceae, and Oscillospiraceae. Several bacteria, including Lactobacillus, Subdoligranulum, Faecalibacterium, Oscillospira, Oscillospiraceae_UCG-002, and Christensenellaceae_R-7_group, could be considered as biomarkers for improving the backfat thickness (BF) for commercial pigs. Additionally, KEGG analysis of gut microbiota further revealed that arginine biosynthesis, pyruvate metabolism, and fatty acid biosynthesis varied greatly among pig breeds. Multiple gut bacterial metabolites (e.g., spermidine, estradiol, and palmitic acid) were identified as breed-associated. Mediation analysis ultimately revealed the cross-talk among gut microbiota, metabolites, and BF thickness, proclaiming that the microbial and metabolic biomarkers identified in this study could be used as biomarkers for improving BF phenotype.ConclusionsThis work provides vital insights into breed effects on gut microbiota and metabolite compositions of commercial pigs and uncovers potential biomarkers that are significant for pig breed improvement.

PSIV-A-3 Effect of fiber and stimbiotic on growth performance and the gut microbiome in pigs challenged with F18 enterotoxigenic Escherichia coli (ETEC)

Abstract Dietary fiber has been shown to promote a healthy gut microbiota, while stimbiotics enhance fermentable substances and boost the expansion of the commensal microbiome, improving host health by alleviating deleterious effects of proinflammatory responses. The intended purpose of this study was to gain an understanding of the effectiveness of dietary fiber sources and stimbiotic on the sustainability of F18 enterotoxigenic Escherichia coli (ETEC) challenge. A total of 216 piglets were blocked (n = 8) by weaning body weight (BW) and randomly assigned to 1 of 4 dietary treatments, including corn-SBM based control diet (CC), high fiber diet (HF: 5.0, 3.8. 2.5% sugar beet pulp and 4.0, 3.0 and 2.0% soy hulls for phases 1, 2, and 3, respectively), CC plus 0.01% stimbiotic (CS: Signis, ABVISTA Marlborough, UK), and HF plus 0.01% stimbiotic (FS). Pigs were fed a four-phase feeding regimen: phase 1 (d 0-9), phase 2 (d 9-16), phase 3 (d 16-22), phase 4 (d 22-41). Dietary fiber and stimbiotic were provided from weaning (d 0) to d 22, and then a common diet was fed from d 22 to the end of the trial. On d 5 postweaning, all pigs were orally inoculated with 10 mL of F18 ETEC (108 CFU/mL). One median BW pig from each pen was selected at weaning for fecal sampling. Before the challenge, the same pigs were sampled on d 5 and again on d 8 and d12. Samples were used to quantify the E. Coli using 3M Petrifilm (3M Food Safety, St. Paul, MN) and virulence genes of the isolate were qualified using multiplex PCR. Colony-forming-count was log-transformed. All data normality was verified using Univariate procedure and analyzed using Mixed procedure of SAS (Cary, NC). Pigs fed both CS and HF increased average daily gain (ADG) in phase 2 and phase 1-3 compared with pigs fed CC diets, while adding stimbiotic had no additional benefit to HF (Fiber×Stimbotic P = 0.03 and 0.06, respectively). This response led to heavier BW in pigs fed CS at the end of phase 3 compared with pigs fed CC with HF and FS as intermediate (Fiber×Stimbotic P = 0.06, respectively). Overall, average daily feed intake (ADFI) was greater in pigs fed CS than pigs fed FS while no difference was found between CC and CF (Fiber×Stimbotic P = 0.02). Dietary fiber did not impact gain to feed ratio (G:F); however, G:F was improved in stimbiotic fed pigs in phase 2 (Stimbiotic P = 0.01). Total coliform count was reduced from d 2 to d 7 (day; P < 0.01), but neither fiber nor stimbiotic altered the coliform count. Results of this study demonstrated that both high fiber and stimbiotic help restore ADG when pigs were challenged with ETEC. Additionally, stimbiotic also benefited feed efficiency and resulted in the heaviest BW.

Gut microbiome and resistome characterization of pigs treated with commonly used post-weaning diarrhea treatments

BackgroundThe global burden of antimicrobial resistance demands additional measures to ensure the sustainable and conscious use of antimicrobials. For the swine industry, the post-weaning period is critical and for many years, antimicrobials have been the most effective strategy to control and treat post-weaning related infections. Among them, post-weaning diarrhea causes vast economic losses, as it severely compromises piglets’ health and growth performance. In this study, 210 piglets were transferred from a farm with recurrent cases of post-weaning diarrhea to an experimental farm and divided into six different treatment groups to determine the effect of the different treatments on the growth performance and survival, the microbiome, and the resistome in a cross-sectional and longitudinal study. The different treatments included antimicrobials trimethoprim/sulfamethoxazole, colistin, and gentamicin, an oral commercial vaccine, a control with water acidification, and an untreated control. An extra group remained at the farm of origin following the implemented amoxicillin routine treatment. A total of 280 fecal samples from pigs at four different sampling times were selected for metagenomics: before weaning-treatment at the farm of origin, and three days, two weeks, and four weeks post-treatment.ResultsThe control group with water acidification showed a reduced death risk in the survival analyses and non-significant differences in average daily weight gain in comparison to the antibiotic-treated groups. However, the growth-promoting effect among antibiotic-treated groups was demonstrated when comparing against the untreated control group at the experimental farm. After four weeks of treatment, diversity indexes revealed significantly decreased diversity for the untreated control and the group that remained at the farm of origin treated with amoxicillin. For this last group, impaired microbial diversity could be related to the continuous amoxicillin treatment carried out at the farm. Analysis of the resistome showed that both gentamicin and amoxicillin treatments significantly contributed to the emergence of resistance, while trimethoprim/sulphonamide and colistin did not, suggesting that different treatments contribute differently to the emergence of resistance.ConclusionsOverall, this shotgun longitudinal metagenomics analysis demonstrates that non-antibiotic alternatives, such as water acidification, can contribute to reducing the emergence of antimicrobial resistance without compromising pig growth performance and gut microbiome.

Influence of Fermented Mulberry Leaves as an Alternative Animal Feed Source on Product Performance and Gut Microbiome in Pigs

Mulberry leaves are rich in nutrients but contain anti-nutrient factors that hinder their digestion and absorption. Feeding animals with mulberry leaves directly could harm their health. The microbial fermentation of mulberry leaves could reduce their anti-nutritional factors’ content and improve their nutritional value. Sequencing and analyzing mulberry leaves before and after fermentation showed that fermentation increased the relative abundance of Pediococcus, Bradyrhizobium, Hydrotalea, and Rhodanobacteria, and decreased that of Enterobacter. Fermentation improved the quality of mulberry leaves by rebuilding the bacterial community. Finishing pigs were raised on fermented mulberry leaves (FML), and their carcass performance, meat quality, economic benefits, and gut microbiome were evaluated. FML had no negative impact on pig carcass performance, meat quality, and antioxidant capacity, and could somewhat improve the economic benefits. FML decreased the relative abundance of Proteobacteria in the colon and Streptococcus in the feces, and increased that of Actinobacteria (cecum, colon, feces) and Prevotella (colon). The gut core microorganisms in the FML group were mainly enriched with Actinobacteria, Bifidobacterium, Bifidobacteriaceae, Bifidobacteriales, and other beneficial microorganisms. Dietary FML reduced ammonia, indole, and skatole contents in the feces. In conclusion, FML reshaped the gut microbiota without negatively affecting pig product performance, produced cleaner waste, and improved environmental protection and sustainability, making it an attractive prospective feed for pigs.

Effect of a probiotic and an antibiotic on the mobilome of the porcine microbiota.

Introduction: To consider the growing health issues caused by antibiotic resistance from a "one health" perspective, the contribution of meat production needs to be addressed. While antibiotic resistance is naturally present in microbial communities, the treatment of farm animals with antibiotics causes an increase in antibiotic resistance genes (ARG) in the gut microbiome. Pigs are among the most prevalent animals in agriculture; therefore, reducing the prevalence of antibiotic-resistant bacteria in the pig gut microbiome could reduce the spread of antibiotic resistance. Probiotics are often studied as a way to modulate the microbiome and are, therefore, an interesting way to potentially decrease antibiotic resistance. Methods: To assess the efficacy of a probiotic to reduce the prevalence of ARGs in the pig microbiome, six pigs received either treatment with antibiotics (tylvalosin), probiotics (Pediococcus acidilactici MA18/5M; Biopower® PA), or a combination of both. Their faeces and ileal digesta were collected and DNA was extracted for whole genome shotgun sequencing. The reads were compared with taxonomy and ARG databases to identify the taxa and resistance genes in the samples. Results: The results showed that the ARG profiles in the faeces of the antibiotic and combination treatments were similar, and both were different from the profiles of the probiotic treatment (p < 0.05). The effects of the treatments were different in the digesta and faeces. Many macrolide resistance genes were detected in a higher proportion in the microbiome of the pigs treated with antibiotics or the combination of probiotics and antibiotics. Resistance-carrying conjugative plasmids and horizontal transfer genes were also amplified in faeces samples for the antibiotic and combined treatments. There was no effect of treatment on the short chain fatty acid content in the digesta or the faeces. Conclusion: There is no positive effect of adding probiotics to an antibiotic treatment when these treatments are administered simultaneously.

Intestinal melatonin levels and gut microbiota homeostasis are independent of the pineal gland in pigs.

Melatonin (MEL) is a crucial neuroendocrine hormone primarily produced by the pineal gland. Pinealectomy (PINX) has been performed on an endogenous MEL deficiency model to investigate the functions of pineal MEL and its relationship with various diseases. However, the effect of PINX on the gastrointestinal tract (GIT) MEL levels and gut microbiome in pigs has not been previously reported. By using a newly established pig PINX model, we detected the levels of MEL in the GIT by liquid chromatography-tandem mass spectrometry. In addition, we examined the effects of PINX on the expression of MEL synthesis enzymes, intestinal histomorphology, and the intestinal barrier. Furthermore, 16S rRNA sequencing was performed to analyze the colonic microbiome. PINX reduced serum MEL levels but did not affect GIT MEL levels. Conversely, MEL supplementation increased MEL levels in the GIT and intestinal contents. Neither PINX nor MEL supplementation had any effect on weight gain, organ coefficient, serum biochemical indexes, or MEL synthetase arylalkylamine N-acetyltransferase (AANAT) expression in the duodenum, ileum, and colon. Furthermore, no significant differences were observed in the intestinal morphology or intestinal mucosal barrier function due to the treatments. Additionally, 16S rRNA sequencing revealed that PINX had no significant impact on the composition of the intestinal microbiota. Nevertheless, MEL supplementation decreased the abundance of Fibrobacterota and increased the abundance of Actinobacteriota, Desulfobacterota, and Chloroflexi. We demonstrated that synthesis of MEL in the GIT is independent of the pineal gland. PINX had no influence on intestinal MEL level and microbiota composition in pigs, while exogenous MEL alters the structure of the gut microbiota.

Maternal Programming of Nursery Pig Performance and Gut Microbiome through Live Yeast Supplementation.

The supplementation of live yeast in pig diets is common in the post-weaning phase due to its prebiotic and probiotic effects, but little is known regarding the potential of feeding live yeast to gestating or lactating sows for transferring such benefits to their offspring through maternal programming. The objective of this study was to investigate the effects of live yeast supplementation in sow diets during late gestation and lactation on their reproductive performance and its impact on offspring performance and gut microbiomes in the post-weaning period. Three dietary treatments were imposed on 92 mixed-parity sows during late gestation and lactation based upon the inclusion level of live yeast in corn/soybean meal-based diets: Control (0% yeast), Low (0.1% yeast), and High (0.5% yeast). Nursery pigs in the Low group displayed the highest feed intake in the post-weaning period and greater total gain and average daily gain in comparison to pigs in the High group. The gut microbiomes of nursery pigs differed in composition according to maternal dietary treatment groups at days 4 and 28 post weaning, highlighting higher abundances of bacterial genera typically associated with fermentation roles in the gut microbiomes of offspring of yeast-fed sows. These results indicate that the supplementation of live yeast in sow diets, depending on the inclusion level, may result in beneficial performance and specific microbiome traits for their offspring in the post-weaning period.

Interactions between maternal parity and feed additives drive the composition of pig gut microbiomes in the post-weaning period

BackgroundNursery pigs undergo stressors in the post-weaning period that result in production and welfare challenges. These challenges disproportionately impact the offspring of primiparous sows compared to those of multiparous counterparts. Little is known regarding potential interactions between parity and feed additives in the post-weaning period and their effects on nursery pig microbiomes. Therefore, the objective of this study was to investigate the effects of maternal parity on sow and offspring microbiomes and the influence of sow parity on pig fecal microbiome and performance in response to a prebiotic post-weaning. At weaning, piglets were allotted into three treatment groups: a standard nursery diet including pharmacological doses of Zn and Cu (Con), a group fed a commercial prebiotic only (Preb) based on an Aspergillus oryzae fermentation extract, and a group fed the same prebiotic plus Zn and Cu (Preb + ZnCu).ResultsAlthough there were no differences in vaginal microbiome composition between primiparous and multiparous sows, fecal microbiome composition was different (R2 = 0.02, P = 0.03). The fecal microbiomes of primiparous offspring displayed significantly higher bacterial diversity compared to multiparous offspring at d 0 and d 21 postweaning (P < 0.01), with differences in community composition observed at d 21 (R2 = 0.03, P = 0.04). When analyzing the effects of maternal parity within each treatment, only the Preb diet triggered significant microbiome distinctions between primiparous and multiparous offspring (d 21: R2 = 0.13, P = 0.01; d 42: R2 = 0.19, P = 0.001). Compositional differences in pig fecal microbiomes between treatments were observed only at d 21 (R2 = 0.12, P = 0.001). Pigs in the Con group gained significantly more weight throughout the nursery period when compared to those in the Preb + ZnCu group.ConclusionsNursery pig gut microbiome composition was influenced by supplementation with an Aspergillus oryzae fermentation extract, with varying effects on performance when combined with pharmacological levels of Zn and Cu or for offspring of different maternal parity groups. These results indicate that the development of nursery pig gut microbiomes is shaped by maternal parity and potential interactions with the effects of dietary feed additives.

Characterizing core microbiota and regulatory functions of the pig gut microbiome.

Domestic pigs (Sus scrofa) are the leading terrestrial animals used for meat production. The gut microbiota significantly affect host nutrition, metabolism, and immunity. Hence, characterization of the gut microbial structure and function will improve our understanding of gut microbial resources and the mechanisms underlying host-microbe interactions. Here, we investigated the gut microbiomes of seven pig breeds using metagenomics and 16S rRNA gene amplicon sequencing. We established an expanded gut microbial reference catalog comprising 17 020 160 genes and identified 4910 metagenome-assembled genomes. We also analyzed the gut resistome to provide an overview of the profiles of the antimicrobial resistance genes in pigs. By analyzing the relative abundances of microbes, we identified three core-predominant gut microbes (Phascolarctobacterium succinatutens, Prevotella copri, and Oscillibacter valericigenes) in pigs used in this study. Oral administration of the three core-predominant gut microbes significantly increased the organ indexes (including the heart, spleen, and thymus), but decreased the gastrointestinal lengths in germ-free mice. The three core microbes significantly enhanced intestinal epithelial barrier function and altered the intestinal mucosal morphology, as was evident from the increase in crypt depths in the duodenum and ileum. Furthermore, the three core microbes significantly affected several metabolic pathways (such as "steroid hormone biosynthesis," "primary bile acid biosynthesis," "phenylalanine, tyrosine and tryptophan biosynthesis," and "phenylalanine metabolism") in germ-free mice. These findings provide a panoramic view of the pig gut microbiome and insights into the functional contributions of the core-predominant gut microbes to the host.

Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population.

Animal ecology and evolution have long been known to shape host physiology, but more recently, the gut microbiome has been identified as a mediator between animal ecology and evolution and health. The gut microbiome has been shown to differ between wild and domestic animals, but the role of these differences for domestic animal evolution remains unknown. Gut microbiome responses to new animal genotypes and local environmental change during domestication may promote specific host phenotypes that are adaptive (or not) to the domestic environment. Because the gut microbiome supports host immune function, understanding the effects of animal ecology and evolution on the gut microbiome and immune phenotypes is critical. We investigated how domestication affects the gut microbiome and host immune state in multiple pig populations across five domestication contexts representing domestication status and current living conditions: free-ranging wild, captive wild, free-ranging domestic, captive domestic in research or industrial settings. We observed that domestication context explained much of the variation in gut microbiome composition, pathogen abundances and immune markers, yet the main differences in the repertoire of metabolic genes found in the gut microbiome were between the wild and domestic genetic lineages. We also documented population-level effects within domestication contexts, demonstrating that fine scale environmental variation also shaped host and microbe features. Our findings highlight that understanding which gut microbiome and immune traits respond to host genetic lineage and/or scales of local ecology could inform targeted interventions that manipulate the gut microbiome to achieve beneficial health outcomes.

Metagenomic Sequencing Analysis of the Effects of Acetylcysteine on the Pig Gut Microbiome

The gut microbiota is engaged in multiple interactions affecting host health, and gut dysbiosis can lead to many diseases. However, the effects of acetylcysteine (NAC) on the gut microbiome composition in pigs using metagenomic sequencing have not been reported. In this study, we used metagenome sequencing to study the effects of NAC on the pig gut microbiome. Sequencing results showed that microbial diversity was changed after NAC treatment. Antibiotic Resistance Genes Database (ARDB) analysis demonstrated that the main genes modified were macb, tsnr, norm, bl2be-per, vansb and pbp1b in the NAC group. Our data showed that NAC could affect microbial distribution at the phylum, gene and species levels. At the species level, NAC significantly increased the abundances of Megasphaera, Lactobacillus reuteri and Megasphaeraelsdenii and reduced the abundances of Phascolarctobacterium succinatutens, Prevotellacopri and Selenomonasbovis compared with the control group. In addition, Gene Ontology (GO) analysis revealed that in the NAC group, cellular process, metabolic process and single-organism process were the dominant terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that RNA transport, MAPK signaling pathway, cell cycle, glycosylphosphatidylinositol (GPI)-anchor biosynthesis and VEGF signaling pathway were the dominant signaling pathways in the NAC group. In conclusion, our results suggest that NAC may modify the piglet gut microbiome composition and these findings might provide a new strategy for maintaining animal and human health in the future.

PSIII-14 Effect of Water Delivery System on Intestinal Microbial Populations of Nursery Pigs

Abstract A previous experiment was conducted to determine if cleanliness of a water delivery system influenced growth performance of nursery pigs. Additionally, we hypothesized that cleanliness of the water delivery system would alter populations of intestinal bacteria. Newly weaned pigs (n = 315; about 21 d of age) were used in a 42-d experiment and were assigned randomly to 1 of 2 water line treatments with 17 to 18 pens/treatment and 9 pigs/pen. Treatments consisted of water delivered to pens via a water distribution system in use for 21 years without cleaning (OLD) or water delivered to pens via a water distribution system in use for 6 weeks (NEW). Water for both distribution systems was sourced from a common well. Pigs were housed in an environmentally controlled, power-ventilated, confinement nursery barn and were allowed ad libitum access to water and common diets fed in 3 phases across OLD and NEW treatments. Twenty-eight pigs of average body weight (n = 14 pigs/treatment) were selected for collection of fecal swabs on days 0, 4, and 42 post-weaning. A pooled water sample was collected from 10 randomly selected pens/treatment and from the water supply on days 4 and 42. Swabs were also collected from the inside surface of each water line at the beginning and end of each line. To characterize the microbiome in all samples, extracted DNA was sequenced on the MiSeq platform targeting the V4 variable region of the 16S rRNA bacterial gene, and sequence data were analyzed using DADA2 and various packages within the R statistical software. Bacterial community composition of water and water line samples differed between OLD and NEW, while the sampling location of line swabs differed by location (PERMANOVA, R2 = 0.2-0.6, P &amp;lt; 0.05). No differences in alpha diversity were observed in pig fecal bacteria at d 0 or d 42 between OLD and NEW line. However, at d 4, pigs drinking water from the NEW line had increased fecal bacterial richness (P = 0.044) and a tendency for increased bacterial diversity (Shannon’s H, P = 0.059) compared with pigs drinking water from the OLD line. There were no differences in bacterial community composition between the OLD and NEW line throughout the trial; however, pigs drinking water from the NEW line showed more discriminating bacterial taxa compared with OLD at day 4 and 42, including greater abundances of Prevotella, Christensenellaceae R7, Rosburia and Bacteroides, among others (P &amp;lt; 0.05). In conclusion, drinking water from either water line did not have major effects on the gut microbiome of pigs, except for more fecal bacterial diversity in pigs drinking water from the new water line at day 4 post-weaning.

Multispecies probiotic supplementation in diet with reduced crude protein levels altered the composition and function of gut microbiome and restored microbiome-derived metabolites in growing pigs.

Both crude protein (CP) and probiotics can modulate the gut microbiome of the host, thus conferring beneficial effects. However, the benefits of low CP diet supplemented with multispecies probiotics on gut microbiome and its metabolites have not been investigated in pigs. Thus, we investigated the combinatory effects of low CP diet supplemented with multispecies probiotics on gut microbiome composition, function, and microbial metabolites in growing pigs. In total, 140 6 week-old piglets (Landrace × Yorkshire × Duroc) were used in this study. The pigs were divided into four groups with a 2 × 2 factorial design based on their diets: normal-level protein diet (16% CP; NP), low-level protein diet (14% CP; LP), NP with multispecies probiotics (NP-P), and LP with multispecies probiotics (LP-P). After the feeding trial, the fecal samples of the pigs were analyzed. The fecal scores were improved by the probiotic supplementation, especially in LP-P group. We also observed a probiotic-mediated alteration in the gut microbiome of pigs. In addition, LP-P group showed higher species richness and diversity compared with other groups. The addition of multispecies probiotics in low CP diet also enhanced gut microbiota metabolites production, such as short-chain fatty acids (SCFAs) and polyamines. Correlation analysis revealed that Oscillospiraceae UCG-002, Eubacterium coprostanoligenes, Lachnospiraceae NK4A136 group, and Muribaculaceae were positively associated with SCFAs; and Prevotella, Eubacterium ruminantium, Catenibacterium, Alloprevotella, Prevotellaceae NK3B31 group, Roseburia, Butyrivibrio, and Dialister were positively correlated with polyamines. Supplementation with multispecies probiotics modulated the function of the gut microbiome by upregulating the pathways for protein digestion and utilization, potentially contributing to enriched metabolite production in the gut. The results of this study demonstrate that supplementation with multispecies probiotics may complement the beneficial effects of low CP levels in pig feed. These findings may help formulate sustainable feeding strategies for swine production.

Comparative analysis of the pig gut microbiome associated with the pig growth performance.

There are a variety of microorganisms in the animal intestine, and it has been known that they play important roles in the host such as suppression of potentially pathogenic microorganisms, modulation of the gut immunity. In addition, the gut microbiota and the livestock growth performance have long been known to be related. Therefore, we evaluated the interrelation between the growth performance and the gut microbiome of the pigs from 3 different farms, with pigs of varied ages ready to be supplied to the market. When pigs reached average market weight of 118 kg, the average age of pigs in three different farms were < 180 days, about 190 days, and > 200 days, respectively. Fecal samples were collected from pigs of age of 70 days, 100 days, 130 days, and 160 days. The output data of the 16S rRNA gene sequencing by the Illumina Miseq platform was filtered and analyzed using Quantitative Insights into Microbial Ecology (QIIME)2, and the statistical analysis was performed using Statistical Analysis of Metagenomic Profiles (STAMP). The results of this study showed that the gut microbial communities shifted as pigs aged along with significant difference in the relative abundance of different phyla and genera in different age groups of pigs from each farm. Even though, there was no statistical differences among groups in terms of Chao1, the number of observed operational taxonomic units (OTUs), and the Shannon index, our results showed higher abundances of Bifidobacterium, Clostridium and Lactobacillus in the feces of pigs with rapid growth rate. These results will help us to elucidate important gut microbiota that can affect the growth performance of pigs.

Cefquinome shows a higher impact on the pig gut microbiome and resistome compared to ceftiofur

Cephalosporins are licensed for treatment of severe bacterial infections in different species. However, the effect of these antimicrobials on the fecal microbiome and potential spread of resistance-associated genes causes great concern. This highlights the need to understand the impact of cephalosporins on the porcine fecal microbiome and resistome. A combination of long-read 16S rRNA gene and shotgun metagenomic sequencing was applied to investigate the effect of conventional treatment with either ceftiofur (3 mg.kg−1 intramuscular, 3 consecutive days) or cefquinome (2 mg.kg−1 intramuscular, 5 consecutive days) on the porcine microbiome and resistome. Fecal samples were collected from 17 pigs (6 ceftiofur treated, 6 cefquinome treated, 5 control pigs) at four different timepoints. Treatment with ceftiofur resulted in an increase in Proteobacteria members on microbiome level, while on resistome level selection in TetQ containing Bacteroides, CfxA6 containing Prevotella and blaTEM-1 containing Escherichia coli was observed. Cefquinome treatment resulted in a decline in overall species richness (α-diversity) and increase in Proteobacteria members. On genus level, administration of cefquinome significantly affected more genera than ceftiofur (18 vs 8). On resistome level, cefquinome resulted in a significant increase of six antimicrobial resistance genes, with no clear correlation with certain genera. For both antimicrobials, the resistome levels returned back to the control levels 21 days post-treatment. Overall, our study provides novel insights on the effect of specific cephalosporins on the porcine gut microbiome and resistome after conventional intramuscular treatment. These results might contribute to better tailoring of the most ideal treatment strategy for some bacterial infections.

P3 | Cefquinome shows a higher impact on the pig gut microbiome and resistome compared to ceftiofur

Journal of Veterinary Pharmacology and TherapeuticsVolume 46, Issue S1 p. 86-86 POSTER PRESENTATIONS P3 | Cefquinome shows a higher impact on the pig gut microbiome and resistome compared to ceftiofur First published: 11 June 2023 https://doi.org/10.1111/jvp.13282Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL No abstract is available for this article. Volume46, IssueS1Special Issue: 15th International Congress of the European Association for Veterinary Pharmacology and Toxicology held Bruges, Belgium, July 2–5, 2023June 2023Pages 86-86 RelatedInformation

Probiotics and Human Milk Differentially Influence the Gut Microbiome and NEC Incidence in Preterm Pigs.

Necrotizing enterocolitis (NEC) is the leading cause of death caused by gastrointestinal disease in preterm infants. Major risk factors include prematurity, formula feeding, and gut microbial colonization. Microbes have been linked to NEC, yet there is no evidence of causal species, and select probiotics have been shown to reduce NEC incidence in infants. In this study, we evaluated the effect of the probiotic Bifidobacterium longum subsp. infantis (BL. infantis), alone and in combination with a human milk oligosaccharide (HMO)-sialylactose (3'SL)-on the microbiome, and the incidence of NEC in preterm piglets fed an infant formula diet. We studied 50 preterm piglets randomized between 5 treatments: (1) Preterm infant formula, (2) Donor human milk (DHM), (3) Infant formula + 3'SL, (4) Infant formula + BL. infantis, and (5) Infant formula and BL. infantis + 3'SL. NEC incidence and severity were assessed through the evaluation of tissue from all the segments of the GI tract. The gut microbiota composition was assessed both daily and terminally through 16S and whole-genome sequencing (WGS) of rectal stool samples and intestinal contents. Dietary BL. infantis and 3'SL supplementation had no effect, yet DHM significantly reduced the incidence of NEC. The abundance of BL. infantis in the gut contents negatively correlated with disease severity. Clostridium sensu stricto 1 and Clostridium perfringens were significantly more abundant in NEC and positively correlated with disease severity. Our results suggest that pre- and probiotics are not sufficient for protection from NEC in an exclusively formula-based diet. The results highlight the differences in microbial species positively associated with both diet and NEC incidence.

Coinfection with porcine epidemic diarrhea virus and Clostridium perfringens type A enhances disease severity in weaned pigs.

Clostridium perfringens is a constituent of the normal gut microbiome in pigs; however, it can potentially cause pre- and post-weaning diarrhea. Nevertheless, the importance of this bacterium as a primary pathogen of diarrhea in piglets needs to be better understood, and the epidemiology of C. perfringens in Korean pig populations is unknown. To study the prevalence and typing of C. perfringens, 203 fecal samples were collected from diarrheal piglets on 61 swine farms during 2021-2022 and examined for the presence of C. perfringens and enteric viruses, including porcine epidemic diarrhea virus (PEDV). We determined that the most frequently identified type of C. perfringens was C. perfringens type A (CPA; 64/203, 31.5%). Among the CPA infections, single infections with CPA (30/64, 46.9%) and coinfections with CPA and PEDV (29/64, 45.3%) were the most common in diarrheal samples. Furthermore, we conducted animal experiments to investigate the clinical outcome of single infections and coinfections with highly pathogenic (HP)-PEDV and CPA in weaned piglets. The pigs infected with HP-PEDV or CPA alone showed mild or no diarrhea, and none of them died. However, animals that were co-inoculated with HP-PEDV and CPA showed more-severe diarrheal signs than those of the singly infected pigs. Additionally, CPA promoted PEDV replication in coinfected piglets, with high viral titers in the feces. A histopathological examination revealed more-severe villous atrophy in the small intestine of coinfected pigs than in singly infected pigs. This indicates a synergistic effect of PEDV and CPA coinfection on clinical disease in weaned piglets.

Perturbations of gut microbiome and metabolome of pigs infected with Mycoplasma hyorhinis.

Mycoplasma hyorhinis is a prevalent respiratory pathogen in swine, causing significant economic loss to pig producers. There is growing evidence that respiratory pathogen infections have a great impact on intestinal microecology. To study the effect of M. hyorhinis infection on gut microbial composition and metabolome profile, we infected pigs with M. hyorhinis and performed metagenomic sequencing analysis of fecal sample and liquid chromatography/tandem mass spectrometry (LC-MS/MS) analysis of gut digesta. RESULTS: It is discovered that pigs infected with M. hyorhinis can enrich Sutterella and Mailhella, and deplete Dechloromonas, Succinatimonas, Campylobacter, Blastocystis, Treponema and Megasphaera. Moreover, the M. hyorhinis infected pigs had higher abundances of bacterium_0_1xD8_71, Ruminococcus_sp__CAG_353, Firmicutes_bacterium_CAG_194, Firmicutes_bacterium_CAG_534, bacterium_1xD42_87, etc., and lower abundances of Chlamydia_suis, Megasphaera_elsdenii, Treponema_porcinum, Bacteroides_sp__CAG_1060, Faecalibacterium_prausnitzii, etc. Metabolomics analysis revealed that some lipids and lipid-like molecules were increased in small intestine, while most of lipids and lipid-like molecules metabolites were decreased in large intestine. These altered metabolites induce changes in intestinal sphingolipid metabolism, amino acid metabolism and thiamine metabolism. These findings demonstrate that the pigs infection with M. hyorhinis can alter the gut microbial composition and metabolites structure, which may further affect amino acid metabolism and lipid metabolism in intestine. This article is protected by copyright. All rights reserved.

Metagenomic and Meta-Transcriptomic Analysis Reveal the Colonization and Expression Profile of Probiotic Strains in Humans and Animals

In humans and animals, probiotics are widely accepted as crucial for host health and growth. The investigation of the probiotic colonization and expression of probiotics in the host is beneficial for proper usage of probiotics and isolation of indigenous probiotics. In this study, we analyzed commonly used probiotic strains in the intestines/rumen of humans and animals by analyzing metagenomic and paired meta-transcriptomic data from the gut or rumen microbiome of humans (n = 13), pigs (n = 6), chickens (n = 6), cattle (n = 14), sheep (n = 10), and mice (n = 8). First, we generated an expression profile based on 192 selected representative probiotic strains from a published database. A total of 58 probiotic strains were not detected in any samples, while 3 strains were presented and expressed in all individuals. Overall, the probiotic expression of probiotics as detected by meta-transcriptome was significantly higher than the relative abundance of probiotic as detected by metagenomics in cattle, sheep, mice, and humans; however, this difference was not significant in pigs and chickens. In total, 17 (cattle), 21 (sheep), 22 (pig), 14 (chicken), 13 (mouse), and 3 (human) probiotic strains were identified as probiotic strains with significantly higher expression levels [Fold Change (FC) ≥ 2, False Discovery Rate (FDR) ≤ 0.05]. Among them, Clostridium butyricum TOA was found to be significantly expressed in the rumen or gut of all host species. In addition, network analysis based on the expression of probiotics as detected by meta-transcriptomics revealed that several probiotic strains were significantly negatively linked with Salmonella spp., Mycoplasma spp., and Escherichia coli. The results in this study provide a useful reference for developing indigenous probiotics.