Development and Function of the Intestinal Microbiome and Potential Implications for Pig Production

Sow Contact Is a Major Driver in the Development of the Nasal Microbiota of Piglets

The nasal microbiota composition is associated with the health status of piglets. Sow-contact in early life is one of the factors influencing the microbial composition in piglets; however, its impact has never been assessed in the nasal microbiota of piglets reared in controlled environmental conditions. Nasal microbiota of weaning piglets in high-biosecurity facilities with different time of contact with their sows (no contact after farrowing, contact limited to few hours or normal contact until weaning at three weeks) was unveiled by 16S rRNA gene sequencing. Contact with sows demonstrated to be a major factor affecting the nasal microbial composition of the piglets. The nasal microbiota of piglets that had contact with sows until weaning, but were reared in high biosecurity facilities, was richer and more similar to the previously described healthy nasal microbiota from conventional farm piglets. On the other hand, the nasal communities inhabiting piglets with no or limited contact with sows was different and dominated by bacteria not commonly abundant in this body site. Furthermore, the length of sow–piglet contact was also an important variable. In addition, the piglets raised in BSL3 conditions showed an increased richness of low-abundant species in the nasal microbiota. Artificially rearing in high biosecurity facilities without the contact of sows as a source of nasal colonizers had dramatic impacts on the nasal microbiota of weaning piglets and may introduce significant bias into animal research under these conditions.

Immunobiotic Feed Developed with Lactobacillus delbrueckii subsp. delbrueckii TUA4408L and the Soymilk By-Product Okara Improves Health and Growth Performance in Pigs

Lactobacillus delbrueckii subsp. delbrueckii TUA4408L is able to differentially modulate the innate immune response of porcine intestinal epithelial cells triggered by TLR4 activation. This strain also has a remarkable ability to grow on plant substrates. These two immunological and biotechnological characteristics prompted us to evaluate whether the soymilk by-product okara fermented with the TUA4408L strain can serve as an immunobiotic feed with the ability to beneficially modulate the intestinal immunity of piglets after weaning to improve their productivity. Our in vivo studies demonstrated that the administration of immunobiotic TUA4408L-fermented okara feed significantly increased piglet growth performance and meat quality. These positive effects were associated with the ability of the TUA4408L-fermented okara feed to beneficially modulate both intestinal microbiota and immunity in pigs. The immunobiotic feed improved the abundance of the beneficial bacteria Lactobacillus and Lactococcus in the gut of pigs, reduced blood markers of inflammation, and differentially regulated the expression of inflammatory and regulatory cytokines in the intestinal mucosa. These findings indicate that the immunobiotic TUA4408L-fermented okara feed could be an economical and environmentally friendly option to improve the growth performance and immune health of pigs.

Characterisation of Early Microbial Colonisers within the Spiral Colon of Pre- and Post-Natal Piglets

Initial enteric microbial colonisation influences animal health and disease, hence an understanding of the first microbial colonisers within the piglet is important. The spiral colon of piglets that were stillborn (n = 20), born-alive (n = 10), and born alive and had sucked (n = 9) were collected from 28 sows to investigate whether initial microbial colonisation occurs pre- or post-partum and how it develops during the first 24 h post-partum. To examine this, DNA was extracted and 16S rRNA amplicon analysis was performed to allow analysis of microbial communities. The results indicate that microbial colonisation of the spiral colon had occurred in stillborn pigs, suggesting microbial exposure prior to birth. Alpha diversity metrics indicated that the number of taxa and community richness were higher in piglets that sucked (p < 0.001) and community evenness was lower in stillborns in comparison to born-alive (p < 0.001) but was not affected by colostrum consumption (p < 0.001). Additionally, when compared with stillborn piglets, the bacteria colonising the spiral colon during the first 24 h post-partum included the potentially pathogenic bacteria Escherichia coli, Clostridium perfringens and Clostridium celatum, and potentially beneficial bacteria Lactobacillus reutueri and Faecalibacterium prausnitzii. The relative presence of Archaea was high in stillborn piglets but decreased with post-natal environmental exposure. It is evident that stillborn piglets have bacteria present within their spiral colon, however further studies are needed in order to determine the time at which colonisation is initiated and the mechanisms determining how colonisation occurs. Additionally, as expected, the immediate post-natal environment largely influences the microorganisms colonising, while colostrum consumption further contributes to the microbial community enrichment.

Gut health: The results of microbial and mucosal immune interactions in pigs

There are a large number of microorganisms in the porcine intestinal tract. These microorganisms and their metabolites contribute to intestinal mucosal immunity, which is of great importance to the health of the host. The host immune system can regulate the distribution and composition of intestinal microorganisms and regulate the homeostasis of intestinal flora by secreting a variety of immune effector factors, such as mucin, secretory immunoglobulin A (sIgA), regenerating islet-derived III (RegIII)γ, and defensin. Conversely, intestinal microorganisms can also promote the differentiation of immune cells including regulatory T cells (T_reg) and Th17 cells through their specific components or metabolites. Studies have shown that imbalances in the intestinal flora can lead to bacterial translocation and compromised intestinal barrier function, affecting the health of the body. This review focuses on the composition of the pig intestinal flora and the characteristics of intestinal mucosal immunity, discusses the interaction mechanism between the flora and intestinal mucosal immunity, as well as the regulation through fecal microbiota transplantation (FMT), dietary nutritional composition, probiotics and prebiotics of pig intestinal microecology. Finally, this review provides insights into the relationship between intestinal microorganisms and the mucosal immune system.

Probiotics mediated gut microbiota diversity shifts are associated with reduction in histopathology and shedding of Lawsonia intracellularis

BACKGROUND

Clinical intervention during bacterial infections in farm animals such as pigs commonly includes the use of antimicrobials. With the rise of antimicrobial resistance and the attempts to reduce the use of antibiotics in food animals, effective alternatives are urgently needed to reduce or even remove pathogens and disease risks. Improving clinical outcomes and overall pig health by using probiotics appears attractive. However, reliable data sets on the efficacy of probiotics are scarce. The obligate intracellular bacterium Lawsonia intracellularis is widespread in pigs and associated with severe enteropathy, mainly in the ileum, commonly resulting in substantial reduction in weight gain. The impact of three in-feed probiotics and a commercial live L. intracellularis vaccine was compared in a pig challenge model. Probiotic treatment was associated with reduced L. intracellularis fecal shedding and reduced gut lesions. Here, the bacterial microbiota of the ileum of these pigs was characterized with 16S rRNA gene sequencing and was subsequently analyzed with bioinformatics tools.

RESULTS

The greatest microbial richness was observed in the probiotic treated group T03-LAW, which accounted for 87% of richness observed in the study. Treatment had a significant impact on both the microbiota structure and taxonomic profile in the ileum, explaining between 26 and 36% of the structural variation, with the strongest association in the T03-LAW group. Overall, the largest changes were observed for the pigs treated with in-feed Bacillus pumilus; the microbiota of these pigs had the greatest diversity and highest richness. We also observed depleted and enriched core microbiota amongst the groups; however, there was no correlation with clinical characteristics. The results suggest that an increased diversity of the ileal microbiota is associated with a reduction in shedding, i.e. a unit increase in Shannon diversity index resulted in 2.8 log reduction in shedding.

CONCLUSIONS

Probiotic supplementation of a base feed ration increased ileum microbiota diversity leading to a mitigation of the effects of a pathogenic L. intracellularis challenge. An even and diverse microbiota community benefits pigs infected with L. intracellularis, however, investigations are needed to determine if this is also true for other pathogens. The study unambiguously demonstrates the usefulness of probiotic supplementation in reducing the impact of enteric pathogens and pathogen shedding rates in food animals without the use of antimicrobials.

Impact of early-life feeding on local intestinal microbiota and digestive system development in piglets

Early-life gut microbial colonisation is known to influence host physiology and development, shaping its phenotype. The developing gastro-intestinal tract of neonatal piglets provides a "window of opportunity" for programming their intestinal microbiota composition and corresponding intestinal development. Here, we investigated the impact of early feeding on jejunum and colon microbiota composition, and intestinal maturation in suckling piglets. From two days of age, early-fed (EF; n = 6 litters) piglets had access to solid feed containing a mixture of fibres till weaning (day29) in addition to sow's milk, whereas the control (CON; n = 6 litters) piglets exclusively fed on sow's milk. Early feeding elicited a significant impact on the colon microbiota, whereas no such effect was seen in the jejunal and ileal microbiota. Quantified eating behavioural scores could significantly explain the variation in microbiota composition of EF piglets and support their classification into good, moderate, and bad eaters. Members of the Lachnospiraceae family, and the genera Eubacterium, Prevotella, and Ruminococcus were quantitatively associated with eating scores. EF piglets were found to have a decreased pH in caecum and colon, which coincided with increased short-chain fatty acid (SCFA) concentrations. Moreover, they also had increased weights and lengths of several intestinal tract segments, as well as a decreased villus-crypt ratio in jejunal mucosa and an increased abundance of proliferative cells in colon mucosa. The approaches in this study indicate that early feeding of a mixed-fibre (pre-weaning) diet changes the microbiota composition, pH, and fermentation products in the distal gut of piglets, while it also alters both macroscopic and microscopic intestinal measurements. These results exemplify the potential of early feeding to modulate intestinal development in young piglets.

A Single Faecal Microbiota Transplantation Altered the Microbiota of Weaned Pigs

Weaning is a stressful time for piglets, often leading to weight loss and is associated with increased morbidity and mortality. A leading cause for these post-weaning problems is enteric dysbiosis and methods to improve piglet health at this crucial developmental stage are needed. This study aimed to determine whether an enteric dysbiosis caused by weaning could be corrected via a faecal microbiota transplantation (FMT) from healthy piglets from a previous wean. Two or four focal piglets per litter were assigned to one of two treatments; FMT two days post weaning (n = 21; FMT) or a control which received saline two days post weaning (n = 21; CON). FMT consisted of homogenised donor faeces administered orally at 3 mL/kg. Weaning occurred at 18 days of age and weights and faecal samples were collected on days 18, 20, 24 and 35. 16S rRNA amplicon analysis was used to assess the faecal microbiota of piglets. FMT increased Shannon’s diversity post weaning (p < 0.001) and reduced the scratch score observed at 24 days of age (p < 0.001). The bacterial populations significantly differed in composition at each taxonomic level. In FMT pigs, significant increases in potentially pathogenic Escherichia coli were observed. However, increases in beneficial bacteria Lactobacillus mucosae and genera Fibrobacteres and Bacteroidetes were also observed in FMT treated animals. To our knowledge, this is the first study to observe a significant effect on piglet faecal microbiota following a single FMT administered post weaning. Therefore, FMT post weaning can potentially alleviate enteric dysbiosis.

Faecal Microbiota Analysis of Piglets During Lactation

Antimicrobial use in animals and the potential development of antimicrobial resistance is a global concern. So, non-antimicrobial techniques for animal disease control are needed. This study aimed to determine whether neonatal ceftiofur (CF) treatment affects piglet faecal microbiomes and whether faecal microbiome transplantation (FMT) can correct it. Two focal piglets per sow were assigned to treatments as follows: cffresh (n = 6) received CF (3 mg/kg intramuscular) at 7 d and fresh FMT at 13 d; cffrozen (n = 7) received CF at 7 d and frozen FMT at 13 d; CF (n = 8) received CF at 7 d and no FMT; and no CF (n = 5) received no CF or FMT. DNA was extracted from faecal samples collected on days 7, 13, and 18 for 16S rRNA amplicon analysis. All faecal blends used for the FMT consisted of pooled donor pig faeces at 1:2 ratio with saline, delivered orally at 3 mL/kg. Alpha and beta diversity metrics increased with age (p < 0.05). However, no effect of antibiotic or FMT treatment was evident in 13 and 18 d old piglets (p > 0.05). Although no effect of treatment was observed, information regarding microbial membership during lactation was gained.

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

Simple Summary

Proper 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.

Abstract

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.

Effects of Three Distinct 2-Week Long Diet Strategies After Transport on Weaned Pigs' Short and Long-Term Welfare Markers, Behaviors, and Microbiota

Alternative feed supplements have shown promising effects in terms of performance, but their effects on welfare have had little evaluation. In the present study, we aimed at evaluating the effect of diet supplementation on welfare indicators. A total of 246 piglets were weaned and transported for 12 h. After transport, they were assigned to one of 3 diets for a 14-day period: A-an antibiotic diet including chlortetracycline and tiamulin, NA-a control diet without any antibiotic or feed supplement, GLN-a diet including 0.20% L-glutamine. After the 14-day period, all piglets were fed the same diet. Tear staining was measured 11 times post-weaning (from d0 to 147). Skin lesions were counted before and after weaning (d-2, 2, and 36). Novel object tests (NOT) were done in groups 4 times post-weaning (d17, 47, 85, 111). Samples for 16S rRNA gene composition were collected prior to transport (d0), following the 14-day period (d14) and at the conclusion of the nursery phase (d34). The NA pigs appeared less interested in novel objects. On d17, they avoided the object less than A pigs (P < 0.05). They spent less time exploring the object on d85 and took longer to interact with the object on d111 than A and GLN pigs (P < 0.05). NA pigs also appeared more sensitive to environment and management. They had larger tear stains than GLN pigs on d84 and 110 (P < 0.05). On d2, NA pigs had more lesions than A and GLN (P < 0.01). In terms of microbiota composition, GLN had higher α-diversity than A and NA (P < 0.001). Differences between dietary treatments were absent at d0, were demonstrated at d14 and disappeared at d34. Pearson correlations between aggression, stress and anxiety indicators and bacterial populations were medium to high from 0.31 to 0.69. The results demonstrate that short-term feeding strategy can have both short- and long-term effects on behavior and welfare, that may partly be explained by changes in gut microbiota composition. Supplementation with GLN appears to confer similar benefits to dietary antibiotics and thus could be a viable alternative.

Dietary Inulin and Trichuris suis Infection Promote Beneficial Bacteria Throughout the Porcine Gut

The gut microbiota (GM) displays a profound ability to adapt to extrinsic factors, such as gastrointestinal pathogens and/or dietary alterations. Parasitic worms (helminths) and host-associated GM share a long co-evolutionary relationship, exerting mutually modulatory effects which may impact the health of the host. Moreover, dietary components such as prebiotic fibers (e.g. inulin) are capable of modulating microbiota toward a composition often associated with a healthier gut function. The effect of helminth infection on the host microbiota is still equivocal, and it is also unclear how parasites and prebiotic dietary components interact to influence the microbiota and host health status. Some helminths, such as Trichuris suis (porcine whipworm), also exhibit strong immunomodulatory and anti-inflammatory effects. We therefore explored the effects of T. suis, alone and in interaction with inulin, both in fecal microbiota during the infection period and luminal microbiota across four intestinal segments at the end of a 4-week infection period. We observed that T. suis generally had minimal, but mainly positive, effects on the microbiota. T. suis increased the relative abundance of bacterial genera putatively associated with gut health such as Prevotella, and decreased bacteria such as Proteobacteria that have been associated with dysbiosis. Interestingly, dietary inulin interacted with T. suis to enhance these effects, thereby modulating the microbiota toward a composition associated with reduced inflammation. Our results show that administration of T. suis together with the consumption of prebiotic inulin may have the potential to positively affect gut health.

Bacillus licheniformis-Fermented Products Reduce Diarrhea Incidence and Alter the Fecal Microbiota Community in Weaning Piglets

Prophylactic use of antibiotics in-feed has been effective in decreasing the incidence of diarrhea in weaning piglets. However, the overuse of antibiotics as prophylactic or therapeutic agents in animal feed leads to the evolution of drug-resistant bacteria and antibiotic residues in pigs. This study investigated the effects of Bacillus licheniformis-fermented products on diarrhea incidence and the fecal microbial community in weaning piglets. A total of 120 crossbred piglets with an average initial body weight of 9.87 ± 1.43 kg were randomly allotted to four dietary treatments consisting of three replicate stalls with 10 piglets in each. The dietary treatments comprised a basal diet as control, control plus 1 g/kg or 4.5 g/kg of B. licheniformis-fermented products, and control plus 30 mg/kg antibiotics (bacitracin methylene disalicylate). Results showed that 4.5 g/kg of B. licheniformis-fermented product supplementation significantly reduced diarrhea incidence in weaning piglets. Principal coordinate analysis and a heatmap of species abundance indicated distinct clusters between the groups treated with antibiotics and B. licheniformis-fermented products. The bacterial richness and evenness in the feces decreased in weaning piglets fed 1 g/kg of B. licheniformis-fermented products and antibiotics. The abundance of the genera [Ruminococcus] gauvreauii group, Ruminococcaceae UCG-005, and Ruminococcaceae UCG-008 in the feces decreased in weaning piglets fed B. licheniformis-fermented products or antibiotics. The average abundance of the genus Prevotella 9 in the feces was positively correlated with the concentration of B. licheniformis-fermented products and negatively correlated with the diarrhea incidence in weaning piglets. Furthermore, the average abundance of the genus Prevotella 9 in the feces was positively correlated with the growth performance of weaning piglets. These results demonstrate that B. licheniformis-fermented products can improve diarrhea incidence and fecal microflora composition in weaning piglets.

The Effect of Increasing Inclusion Levels of a Fucoidan-Rich Extract Derived from Ascophyllum nodosum on Growth Performance and Aspects of Intestinal Health of Pigs Post-Weaning

This study examines the effects of increasing dietary inclusion levels of fucoidan, from a 44% fucoidan extract on the growth performance and intestinal health of pigs post-weaning (PW). Seventy-two newly weaned pigs (8.4 kg (SD 1.06)) were assigned to: (T1) basal diet (BD); (T2) BD + 125 ppm fucoidan; (T3) BD + 250 ppm fucoidan (8 pens/treatment). The appropriate quantity of a 44% fucoidan extract was included to achieve these inclusion levels. Faecal scores were recorded daily. On d15 PW, samples were collected from the intestinal tract from 1 pig/pen from the BD and BD + 250 ppm fucoidan groups. Pigs supplemented with 250 ppm fucoidan had improved faecal scores and increased concentrations of total volatile fatty acids and propionate in the colon (p < 0.05). The fucoidan-rich extract reduced the expression of CLDN5 (duodenum), SCL5A1/SGLT1 and SI (jejunum) and TJP1, FABP2, and SLC5A1 (ileum) (p < 0.05). The extract reduced the relative abundance of Prevotella and Lachnospiraceae (p < 0.05) and increased the abundance of Helicobacter (p < 0.01) in the caecum. However, no negative impact on growth performance or small intestinal morphology was observed. Thus, the inclusion of 250 ppm fucoidan improves faecal consistency without affecting growth performance and therefore warrants further investigation as a supplement for the prevention of PW diarrhoea under more challenging commercial conditions.

Preliminary Study: Depriving Piglets of Maternal Feces for the First Seven Days Post-Partum Changes Piglet Physiology and Performance before and after Weaning

Simple Summary

Coprophagy is the behavior of eating feces. This behavior has been reported in many animals, including pigs. We aimed to assess how coprophagy affects piglet behavior, physiology, and performance by depriving piglets of maternal feces for the first 7 d post-partum. Eight litters were randomly assigned either to have access to maternal feces (control) or to be deprived of maternal feces for the first 7 d post-partum. Piglet behavior was observed for 24 h at 7 d of age and two piglets from each litter (male and female) were bled for hematological analysis at 0, 7, and 21 d of age. Piglets feed intake and weight gain were measured until 123 d post-weaning. No behavioral differences were observed between treatments. Overall, control piglets had 25% higher white blood cell counts and higher feed intake and weight gain than piglets deprived of maternal feces. At 123 d post-weaning, control piglets were 9.6 kg heavier than piglets deprived of maternal feces. In conclusion, piglets with access to maternal feces early in life exhibited better performance. The mechanisms by which coprophagy improves piglet performance needs to be elucidated in further studies, but could include effects of the nutrition, microbiome or semiochemical exposure.

Abstract

Coprophagy has been described in piglets although its importance has not been fully assessed. The aim of this study was to evaluate how deprivation of maternal feces influenced piglet physiology, behavior, and performance. Eight litters were randomly assigned to one of two treatments. Control (CON) litters had access to maternal feces while deprived (DEP) litters were deprived of maternal feces for the first 7 d post-partum. Piglet behavior was quantified for 24 h at 7 d of age. Blood samples were collected from one male and female from each litter at 0, 7, and 21 d for hematological analyses, and post-weaning performance was assessed until 123 d post-weaning. No treatment effects were observed on piglet behavior. DEP piglets had 25% lower leukocyte counts (p < 0.01). Relative to DEP litters, CON litters had increased post-weaning feed intake (0.998 vs 0.901 kg/d; p = 0.02) and weight gain (0.536 vs 0.483 kg/d; p < 0.01). At 123 d post-weaning, CON pigs were 9.3 ± 2.3 kg heavier than treatment pigs (p < 0.01). These results suggest that access to maternal feces improves immunocompetence and growth performance. Further studies are needed to explore the physiological mechanisms through which maternal feces improve growth performance, including nutritional and microbial factors, or the presence of maternal semiochemicals.