Microbiome In Pigs Research Articles

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.

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.

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.

275 Awardee Talk: Gnotobiotic Porcine Models to Better Understand Gut Microbiome-Host Interactions in Human and Porcine Hosts

Abstract Better understanding the interactions between the gut microbiome and its host is at the forefront of research conducted in areas related to human health as well as livestock production. The complexity of the gut microbiome as well as the numerous environmental and host factors that influence the structure and function of the microbial community complicates the study of host-gut microbiome interactions under natural conditions. To this end, germ-free animal models which have been transplanted with target microbiomes and raised under controlled experimental conditions provide a unique opportunity to mitigate some of the inherent difficulties related to studying host-microbiome interactions in conventional animals as well as in humans. Due to its high degree of similarity to humans at the anatomical, biochemical, and immunological levels and its importance in the livestock industry, the domestic pig (Sus scrofa domesticus) is an excellent animal model which has a unique ‘dual-purpose’ potential for use in both human health and livestock production research. Using high-throughput DNA sequencing technologies, we have demonstrated some of the advantages of using human microbiota-associated (HMA) porcine models compared with commonly used HMA mouse models to study the human gut microbiome. Specifically, we identified that a significantly greater percentage of taxa from child, adult, and senior donors were able to colonize (69% to 85% in pigs versus 41% to 49% in mice) and persist (28% to 57% in piglets versus 21% to 28% in mice) in the HMA piglets compared with the HMA mice, and that this was primarily driven by a greater colonization success of Firmicutes members in the pigs compared with the mice. In addition, we have characterized human infant microbiota-associated porcine models at both the taxonomic and functional levels to better understand the HMA piglet as a model for infant microbiome investigations. We have also utilized the porcine microbiota-associated (PMA) pig model to understand the establishment and development of the porcine gut microbiome. This model has great potential to dissect the mechanistic relationship between the host and its microbiome in pigs. Additionally, this model can be used to understand how prebiotics and direct-fed microbials might interact with the gut microbiome and influence porcine health and well-being. Despite some of the challenges to the widespread use of gnotobiotic porcine models, such as high overhead costs and labor involved in animal care, the porcine model holds a lot of promise to help better understand host-gut microbiome interactions.

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.

Longitudinal analysis of the faecal microbiome in pigs fed Cyberlindnera jadinii yeast as a protein source during the weanling period followed by a rapeseed- and faba bean-based grower-finisher diet.

The porcine gut microbiome is central to animal health and growth as well as it can be structurally or functionally reshaped by dietary interventions. The gut microbiota composition in relation to Cyberlindnera jadinii yeast as a protein source in a weanling diet was studied previously. Also, there is a mounting body of knowledge regarding the porcine gut microbiome composition in response to the use of rapeseed (Brassica napus subsp. napus) meal, and faba beans (Vicia faba) as protein sources during the growing/finishing period. However, there is limited data on how the porcine gut microbiome respond to a combination of C. jadinii yeast in the weanling phase and rapeseed meal and faba beans in the growing/finishing phase. This work investigated how the porcine faecal microbiome was changing in response to a novel yeast diet with a high inclusion of yeast proteins (40% of crude protein) in a weanling diet followed by a diet based on rapeseed meal and faba beans during the growing/finishing period. The faecal microbiomes of the weanling pigs fed yeast were more diverse with higher relative abundance of Firmicutes over Bacteroidetes compared with those of soybean meal-based diet fed weanlings. Reduced numbers of Prevotella in the yeast fed faecal microbiomes remained a microbiome characteristic up until two weeks after the yeast diet was changed to the rapeseed/faba bean growing finishing diet. A number of differentially abundant bacterial phylotypes along with distinct co-occurrence patterns observed during the growing/finishing period indicated the presence of a "carry-over" effect of the yeast weanling diet onto the faecal microbiomes of the grower/finisher pigs.

Remodeling of the maternal gut microbiome during pregnancy is shaped by parity

BackgroundThe maternal microbiome has emerged as an important factor in gestational health and outcome and is associated with risk of preterm birth and offspring morbidity. Epidemiological evidence also points to successive pregnancies—referred to as maternal parity—as a risk factor for preterm birth, infant mortality, and impaired neonatal growth. Despite the fact that both the maternal microbiome and parity are linked to maternal-infant health, the impact of parity on the microbiome remains largely unexplored, in part due to the challenges of studying parity in humans.ResultsUsing synchronized pregnancies and dense longitudinal monitoring of the microbiome in pigs, we describe a microbiome trajectory during pregnancy and determine the extent to which parity modulates this trajectory. We show that the microbiome changes reproducibly during gestation and that this remodeling occurs more rapidly as parity increases. At the time of parturition, parity was linked to the relative abundance of several bacterial species, including Treponema bryantii, Lactobacillus amylovorus, and Lactobacillus reuteri. Strain tracking carried out in 18 maternal-offspring “quadrads”—each consisting of one mother sow and three piglets—linked maternal parity to altered levels of Akkermansia muciniphila, Prevotella stercorea, and Campylobacter coli in the infant gut 10 days after birth.ConclusionsCollectively, these results identify parity as an important environmental factor that modulates the gut microbiome during pregnancy and highlight the utility of a swine model for investigating the microbiome in maternal-infant health. In addition, our data show that the impact of parity extends beyond the mother and is associated with alterations in the community of bacteria that colonize the offspring gut early in life. The bacterial species we identified as parity-associated in the mother and offspring have been shown to influence host metabolism in other systems, raising the possibility that such changes may influence host nutrient acquisition or utilization. These findings, taken together with our observation that even subtle differences in parity are associated with microbiome changes, underscore the importance of considering parity in the design and analysis of human microbiome studies during pregnancy and in infants.EiSDZE1QSYbum5s8Ch3ZCDVideo abstract

Replacing dietary antibiotics with 0.20% l-glutamine in swine nursery diets: impact on intestinal physiology and the microbiome following weaning and transport.

Previous research demonstrates that supplementing 0.20% l-glutamine (GLN) in the diets of newly weaned and transported pigs improves growth rate to a similar extent as providing dietary antibiotics (AB). However, research comparing the effects of GLN vs. AB on intestinal physiology and the microbiome is limited. Therefore, the study objective was to compare the effects of supplementing nursery diets with GLN, AB, or no dietary antibiotics (NA) on intestinal physiology and the microbiome of pigs in a production environment following weaning and transport. Mixed-sex piglets (N = 480; 5.62 ± 0.06 kg body weight [BW]) were weaned (18.4 ± 0.2 d of age) and transported for 12 h in central Indiana, for two replicates, during the summer of 2016 and the spring of 2017. Pens were blocked by BW and allotted to one of the three dietary treatments (n = 10 pens/dietary treatment/replicate [8 pigs/pen]): AB (chlortetracycline [441 ppm] + tiamulin [38.6 ppm]), GLN (0.20% as-fed), or NA fed for 14 d. From day 14 to 34, pigs were fed common AB-free diets in two phases. On day 33, villus height:crypt depth tended to be increased (P = 0.07; 7.0%) in GLN and AB pigs vs. NA pigs. On day 33, glucagon-like peptide 2 (GLP-2) mRNA abundance was decreased (P = 0.01; 50.3%) in GLN and NA pigs vs. AB pigs. Crypt depth was increased overall on day 33 (P = 0.01; 16.2%) during the spring replicate compared with the summer replicate. Villus height:crypt depth was reduced (P = 0.01; 9.6%) during the spring replicate compared with the summer replicate on day 33. On day 13, tumor necrosis factor-alpha and occludin mRNA abundance was increased (P ≤ 0.04; 45.9% and 106.5%, respectively) and zonula occludens-1 mRNA abundance tended to be greater (P = 0.10; 19.2%) in the spring replicate compared with the summer replicate. In addition, AB pigs had increased (P = 0.01; 101.3%) GLP-2 mRNA abundance compared with GLN and NA pigs. Microbiome analysis indicated that on day 13, dietary treatment altered the microbiota community structure (P = 0.03). Specifically, the AB pigs tended to be distinct from both the NA and GLN pigs (P = 0.08), and Lactobacillus was increased nearly 2-fold in AB compared with NA pigs (q = 0.04) and GLN pigs (q = 0.22). In conclusion, GLN supplementation tended to improve some morphological markers of intestinal health similarly to AB pigs, while the microbiome composition in GLN pigs was more similar to NA pigs than AB pigs.

Relationships among Fecal, Air, Oral, and Tracheal Microbial Communities in Pigs in a Respiratory Infection Disease Model.

The association of the lower respiratory tract microbiome in pigs with that of other tissues and environment is still unclear. This study aimed to describe the microbiome of tracheal and oral fluids, air, and feces in the late stage of Mycoplasma hyopneumoniae infection in pigs, and assess the association between the tracheal microbiome and those from air, feces, and oral fluids. Tracheal fluids (n = 73), feces (n = 71), oropharyngeal fluids (n = 8), and air (n = 12) were collected in seeder pigs (inoculated with M. hyopneumoniae) and contact pigs (113 days post exposure to seeder pigs). After DNA extraction, the V4 region from 16S rRNA gene was sequenced and reads were processed using Divisive Amplicon Denoising Algorithm (DADA2). Clostridium and Streptococcus were among the top five genera identified in all sample types. Mycoplasma hyopneumoniae in tracheal fluids was associated with a reduction of diversity and increment of M. hyorhinis, Glaesserella parasuis, and Pasteurella multocida in tracheal fluids, as well as a reduction of Ruminiclostridium, Barnesiella, and Lactobacillus in feces. Air contributed in a greater proportion to bacteria in the trachea compared with feces and oral fluids. In conclusion, evidence suggests the existence of complex interactions between bacterial communities from distant and distinct niches.

Advanced Digestion Enhancing Protein Plus Technology (ADEPPTTM) for assisting the restoration of the Gut Microbiome in Pigs with diarrhea

BackgroundThe microbiome of the gastrointestinal tract (GIT) is a dynamic system, susceptible to a variety of factors including environmental stress and diet. The gut microbiome consists of diverse microbiota that plays an important role in physiological functions. Studies have demonstrated that the most important period for microbial establishment is early life when suckling and weaning. Due to changes in rations, many piglets suffer from enteritis, which may lead to diarrhea, dehydration, and death. Hence, microbiome and healthy gut play important roles in swine production. The effect of nutraceuticals for the development, maintenance, and restoration of the gut microbiome in piglets with diarrhea needs to be explored.AimTo evaluate the effect of ADEPPTTM (a naturally derived polypeptide and polysaccharide complex) for restoration of the gut microbiome in pigs with diarrhea.Methods28‐day‐old suckling piglets were segregated for solid foods in a pig farm at the University of WI‐River Falls. The pigs were fed corn‐soybean based diet and some piglets had diarrhea within 2 to 3 days. Fecal samples were collected from the piglets (without diarrhea as the control, piglets during and after diarrhea) and stored at −80°C. Electrolytes were given to all and ADEPPT (3g/day) only to diarrhea group for a week. DNA was extracted from feces using the PowerSoil DNA extraction kit and sent to the University of Minnesota Genomic Center. The V4 variable region of the bacterial 16S rRNA gene was amplified and libraries were constructed using a dual index approach1. 16SrRNA libraries were sequenced on a MiSeq V3, targeting 2×300 PE reads. Processing of amplicons was based on in‐house protocols that rely on several open‐source software to remove adaptors and primer sequences, merge PE reads, filter out low quality reads, and count unique Amplicon sequence Variants (ASVs) or unique taxonomic groups that represent the abundance of species and/or strains in each sample. All statistical analyses including alpha and beta diversity, estimation, and indicator species were performed using various packages in the R statistical interface.ResultsAn average of 53,965 ± 9,808 sequence reads per sample were obtained. Differences were found in terms of bacterial community richness and Shannon index diversity between control, diarrhea, and after treatment with ADEPPT. In addition, the microbiomes of the treated group significantly discriminated based on a Bray‐Curtis distance PCoA. Indicator species analyses showed the ASVs or bacterial species/strains that best discriminated among treatment groups. The control samples revealed increased abundance of unclassified Synergistaceae, Bacteroides ovatus, Eubacterium, and Bacteroidales. The diarrhea samples were characterized by increased abundance of unclassified Veilloneaceae, Entreobacteriaceae, Paraprevotellaceae, and Treponema. The ADEPPT‐treated samples demonstrated higher abundance of Faecalibacterium prausnitzii, unclassified Ruminococcus and Ruminococcus gnavus. There is a lower diversity in diarrhea samples which recovered by treating with ADEPPT.ConclusionThese findings suggest that ADEPPTTM assists the restoration of the gut microbiome in weaned pigs with diarrhea.

Development of Swine's Digestive Tract Microbiota and Its Relation to Production Indices-A Review.

Simple SummaryProper cooperation between digestive system microbiota and the host is an important issue in maintaining proper health condition, and—in the case of farm animals—production indices. In the case of pigs, microbiota significantly affect production parameters such as meat quality, growth rate or improvement of immune response to infections. Understanding of pig digestive system microbiota and factors affecting this is an important issue. This may enable improvement of animal performance and stabilization of microbiota during their growth, reducing the risk of metabolic or systemic diseases.The development of research methods and tools related to microbiome investigation, as well as widened knowledge and awareness concerning the significance of microorganisms inhabiting mammalian organisms, has led to an increasing popularity of studies in this field. This review paper presents some issues related to the swine microbiome, its development starting from an early age of life and its status in adult animals, as well as factors affecting the microbiome in pigs. Attention is paid to the role of probiotics and prebiotics as alternatives to antibiotics in the context of post-weaning diarrhea treatment, and to the role of microorganisms inhabiting the digestive tract of pigs in performance indices formation. In veterinary and pork production practice, understanding of the swine microbiome and its relationships with the host organism may be useful in the prevention of some diseases and also in improvement of performance results of animals.

Bioregional Alterations in Gut Microbiome Contribute to the Plasma Metabolomic Changes in Pigs Fed with Inulin.

Inulin (INU) is a non-digestible carbohydrate, known for its beneficial properties in metabolic disorders. However, whether and how gut microbiota in its regulation contributes to host metabolism has yet to be investigated. We conduct this study to examine the possible associations between the gut microbiota and circulating gut microbiota–host co-metabolites induced by inulin interventions. Plasma and intestinal site samples were collected from the pigs that have consumed inulin diet for 60 days. High-throughput sequencing was adopted for microbial composition, and the GC-TOF-MS-based metabolomics were used to characterize featured plasma metabolites upon inulin intervention. Integrated multi-omics analyses were carried out to establish microbiota–host interaction. Inulin consumption decreased the total cholesterol (p = 0.04) and glucose (p = 0.03) level in serum. Greater β-diversity was observed in the cecum and colon of inulin-fed versus that of control-fed pigs (p < 0.05). No differences were observed in the ileum. In the cecum, 18 genera were altered by inulin, followed by 17 in the colon and 6 in the ileum. Inulin increased propionate, and isobutyrate concentrations but decreased the ratio of acetate to propionate in the cecum, and increased total short fatty acids, valerate, and isobutyrate concentrations in the colon. Metabolomic analysis reveals that indole-3-propionic acid (IPA) was significantly higher, and the branched-chain amino acids (BCAA), L-valine, L-isoleucine, and L-leucine are significantly lower in the inulin groups. Mantel test and integrative analysis revealed associations between plasma metabolites (e.g., IPA, BCAA, L-tryptophan) and inulin-responsive cecal microbial genera. These results indicate that the inulin has regional effects on the intestine microbiome in pigs, with the most pronounced effects occurring in the cecum. Moreover, cecum microbiota plays a pivotal role in the modulation of circulating host metabolites upon inulin intervention

171 Fecal microbiota transplant at weaning improves growth performance and alters fecal microbiome in pigs

Abstract To evaluate the effect of fecal microbiota transplant (FMT) on the growth performance and fecal microbiome, a total of 24 weaned pigs were stratified by weaning BW and sex, and assigned to one of two groups: a) Control (20% glycerol); b) FMT (from a healthy-grower-stage-no-antibiotics-treated pig). Microbiota mixture or placebo were drenched to pigs for two consecutive days after weaning (d-0 and -1). All pigs were fed antibiotics-free diets for an 8 feeding phase regimes: nursery phase 1, 2, and 3 (0–8, 8–21 and 21–40 d, respectively); finisher phase 1, 2, 3, 4, and 5 (40–63, 63–78, 78–117, 117–138, and 138–166 d, respectively). Individual pig BW was recorded at each phase change, and FOMeater data were collected at the end of trial. Growth and carcass data were analyzed by GLM procedure of SAS (Cary, NC) as CBD. Rectal swabs were collected prior to treatment, on d 1 &amp; 2, and at each phase change. DNA was extracted from these swabs, amplified by primers targeting the V4 region of the 16S rDNA gene, and sequenced using an Illumina MiSeq sequencer. Sequences were classified against Ribosomal Database Project using Mothur (v.1.42) package. Pigs received FMT tended to have greater weight gain during finisher phase 1 (1.05 vs 0.91 kg/d, P = 0.07), and heavier HCW (105.5 vs 97.6 kg, P = 0.09) than control. PCoA plot based on the Jaccard distance shows that FMT pigs microbiota community was not different from control pigs until the end of nursery phase 2 (ANOSIM, R = 0.237, P &amp;lt; 0.01) and 3 (R = 0.241, P = 0.01). Classification-based Random Forest revealed that OTU3 Streptococcus (d 3, 63, 117) and OTU95 Selenomonas (d 8, 21) were more abundant in the FMT pigs than in control pigs. Results suggests that FMT at weaning age from grower stage pig donor modulate microbiome and improve growth performance.

Diversity and community of methanogens in the large intestine of finishing pigs

BackgroundMethane emissions from pigs account for 10% of total methane production from livestock in China. Methane emissions not only contribute to global warming, as it has 25 times the global warming potential (GWP) of CO2, but also represent approximately 0.1~3.3% of digestive energy loss. Methanogens also play an important role in maintaining the balance of the gut microbiome. The large intestines are the main habitat for the microbiome in pigs. Thus, to better understand the mechanism of methane production and mitigation, generic-specific and physio-ecological characteristics (including redox potential (Eh), pH and volatile fatty acids (VFAs)) and methanogens in the large intestine of pig were studied in this paper. Thirty DLY finishing pigs with the same diet and feeding conditions were selected for this experiment.ResultA total of 219 clones were examined using the methyl coenzyme reductase subunit A gene (mcrA) and assigned to 43 operational taxonomic units (OTUs) based on a 97% species-level identity criterion. The family Methanobacteriaceae was the dominant methanogen in colonic digesta of finishing pigs, accounting for approximately 70.6% of the identified methanogens, and comprised mainly the genera Methanobrevibacter (57%) and Methanosphaera (14%). The order Methanomassiliicoccales, classified as an uncultured taxonomy, accounted for 15.07%. The methanogenic archaeon WGK1 and unclassified Methanomicrobiales belonging to the order of Methanomicrobiales accounted for 4.57 and 1.37%, respectively. The Eh was negative and within the range − 297.00~423.00 mV and the pH was within the range 5.04~6.97 in the large intestine. The populations of total methanogens and Methanobacteriales were stable in different parts of the large intestine according to real-time PCR.ConclusionThe major methanogen in the large intestine of finishing pigs was Methanobrevibacter. The seventh order Methanomassiliicoccales and species Methanosphaera stadtmanae present in the large intestine of pigs might contribute to the transfer of hydrogen and fewer methane emissions. The redox potential (Eh) was higher in the large intestine of finishing pigs, which had a positive correlation with the population of Methanobacteriale.

Development of the Tonsil Microbiome in Pigs and Effects of Stress on the Microbiome.

Tonsils, lympho-epithelial tissues located at the junction of the oropharynx and nasopharynx, play a key role in surveillance, colonization, and persistence of inhaled and ingested pathogens. In pigs, the tonsils are a reservoir for numerous bacteria and viruses, including host-specific pathogens and potential zoonotic pathogens as well as commensal organisms. However, there are no in depth studies of the development of the tonsillar microbiome in pigs, or any mammal, over time. The goal of this study was to follow the development of the tonsil microbiome in healthy pigs from birth to market weight. Samples were collected using tonsil brushes from 16 piglets (4 each from 4 sows) at newborn, 1, 2, 3, and 4 weeks of age, and from 8 of those piglets at 6, 8, 10, 12, 16, and 19 weeks of age. Bacterial DNA was isolated from each sample and 16S rDNA genes were amplified and sequenced. Sequence analysis showed that members of the Streptococcaceae, Pasteurellaceae, and Moraxellaceae were present at all time points and represent the three most abundant families identified. Other community members appeared transiently or increased or decreased significantly with disruption events or stress. We observed four significant shifts in the tonsil community that coincided with well-defined disruption events: weaning plus addition of Carbadox plus movement to the nursery at week 3, removal of Carbadox and addition of Tylan at week 5, removal of Tylan and habitat change at week 9, and habitat change at week 16. Weaning triggered a bloom of Streptococcaeae and decrease of Moraxellaceae. The shift from Carbadox to Tylan led to reduction in Proteobacteria and Streptococcaceae but an increase in other Firmicutes, accompanied by a dramatic increase in community richness. Cessation of Tylan coincided with a return to a less rich community, and a bloom in Clostridiales. The final shift in habitat was accompanied by a decrease in Clostridiales and increase in Proteobacteria. The tonsillar microbiome of older pigs resembled the previously described mature core tonsillar microbiome. This study demonstrates a temporal succession in the development of the pig tonsillar microbiome, and significant community shifts that correlate with disruption events.

Development of the tonsillar microbiome in pigs from newborn through weaning

BackgroundPorcine tonsils are lympho-epithelial tissues, colonized by numerous bacteria and viruses, that act as a reservoir for both host-specific pathogens and zoonotic pathogens with a high potential of transmission to humans. There are no existing studies describing the development of the tonsillar microbiome. We sequenced 16S rRNA genes from tonsillar samples of pigs to follow the development of the microbial communities from birth through weaning. Samples derived from sows were also analyzed to determine potential sources for the tonsil microbiome in piglets.ResultsThe composition of the newborn piglet tonsil microbiome could be differentiated by litter and had strong similarity to the sow teat skin as well as sow vaginal microbiome. The tonsil microbiome in these young piglets was mainly dominated by members of the Pasteurellaceae, Moraxellaceae, and Streptococcaceae families, while there were some transient members of the microbiome that were abundant at specific times, such as Staphylococcaceae in newborns and Fusobacteriaceae and Leptotrichiaceae in weeks 2 and 3. The microbiome initially differed between litters but over the following 3 weeks the communities of different litters converged in composition and then diverged in week 4 due to a combination of changes and stresses associated with weaning, including a shift from milk to a solid diet, in-feed Carbadox® and room change.ConclusionsA significant portion of the tonsil microbiome was acquired either at birth from the sow vaginal tract or within a few hours post-birth from the sow teat skin. Our data demonstrate a temporal succession in the development of the pig tonsillar microbiome through the first weeks of life, with a convergence in the composition of the microbiome in all piglets by 3 weeks of age. The combination of management practices associated with weaning coincided with dramatic shifts in the tonsillar microbiome.

Early Postnatal Diets Affect the Bioregional Small Intestine Microbiome and Ileal Metabolome in Neonatal Pigs

BackgroundBreastfeeding is known to be protective against gastrointestinal disorders and may modify gut development. Although the gut microbiome has been implicated, little is known about how early diet affects the small intestine microbiome. ObjectiveWe hypothesized that disparate early diets would promote unique microbial profiles in the small intestines of neonatal pigs. MethodsMale and female 2-d-old White Dutch Landrace pigs were either sow fed or provided dairy (Similac Advance powder; Ross Products Abbott Laboratories) or soy (Enfamil Prosobee Lipil powder; Mead Johnson Nutritionals) infant formulas until day 21. Bacterial ecology was assessed in the contents of the small intestine through the use of 16S ribosomal RNA sequencing. α-Diversity, β-diversity, and differential abundances of operational taxonomic units were assessed by ANOVA, permutational ANOVA, and negative binomial regression, respectively. Ileum tissue metabolomics were measured by LC-mass spectrometry and assessed by weighted correlation network analysis. ResultsGreater α-diversity was observed in the duodena of sow-fed compared with formula-fed neonatal pigs (P < 0.05). No differences were observed in the ilea. Firmicutes represented the most abundant phylum across all diets in duodena (78.8%, 80.1%, and 53.4% relative abundance in sow, dairy, and soy groups, respectively), followed by Proteobacteria in sow (12.2%) and dairy (12.4%) groups and Cyanobacteria in soy-fed (36.2%) pigs. In contrast to those in the duodenum, Proteobacteria was the dominant phylum in the ileum, with >60% relative abundance in all of the groups. In the duodenum, 77 genera were altered by diet, followed by 48 in the jejunum and 19 in the ileum. Metabolomics analyses revealed associations between ileum tissue metabolites (e.g., acylcarnitines, 3-aminoisobutyric acid) and diet-responsive microbial genera. ConclusionsThese results indicate that the neonatal diet has regional effects on the small intestine microbiome in pigs, with the most pronounced effects occurring in the duodena. Regional effects may be important factors when considering gut tissue metabolism and development in the postnatal period.

Importance of the fat content within the cheese-matrix for blood lipid profile, faecal fat excretion, and gut microbiome in growing pigs

Cheese and butter have been shown to affect blood lipids differently. This parallel-arm, randomised, controlled study in 36 crossbred growing sows compared the effect of diets with either regular-fat cheese (REG), reduced-fat cheese + butter (RED) or butter (BUT) on blood lipids, faecal fat and energy excretion and gut microbiome in pigs. A 14-d run-in period was followed by 14-d interventions with macronutrient-matched diets. Fasting total cholesterol and HDL-cholesterol after 14 days were higher in REG compared with BUT, but only tended to be higher in RED. Compared with BUT, REG and RED had higher faecal fat excretion. Faecal energy excretion was only higher in REG, and this correlated with a lower microbiome Firmicutes-to-Bacteroidetes ratio. In conclusion, dairy fat consumed as cheese or butter caused different metabolic effects. Differences between reduced-fat cheese+butter and butter were less pronounced than differences between regular-fat cheese and butter, suggesting an impact of the dairy-matrix.

THU-403 - Influence of Acute Failure on the Structure of GUT Microbiome in Pigs

THU-403 - Influence of Acute Failure on the Structure of GUT Microbiome in Pigs