Effect of inulin supplementation on selected gastric, duodenal, and caecal microbiota and short chain fatty acid pattern in growing piglets

Different Physiochemical Properties of Novel Fibre Sources in the Diet of Weaned Pigs Influence Animal Performance, Nutrient Digestibility, and Caecal Fermentation

The effect of including micronised fibre sources (FS) differing in fermentability and hydration capacity (HC) on growth performance, faecal digestibility, and caecal fermentation was investigated in piglets. There were four dietary treatments: a control diet (CON) and three treatments differing in the HC and fermentability of FS added at 1.5% to prestarter (28-42 d) and starter (42-61 d) diets. These were: LHC (low-HC by-product-based insoluble fibre (IF) with a prebiotic fraction (PF) from chicory root); MHC (medium-HC by-product-based IF with a PF); and HHC (high-HC non-fermentable wood-based IF with no PF). There were eight replicates per treatment. Over the entire period, LHC and MHC piglets showed a 10% increase in daily growth and feed intake (p ≤ 0.019) and tended to have a reduced feed conversion ratio (p = 0.087) compared to HHC piglets. At 42 d, faecal protein digestibility increased by 5% in the LHC and MHC groups compared with the HHC group (p = 0.035) and did not differ from the CON group. Both LHC and MHC fibres were more fermented in vitro with caecal inocula from 61 d old piglets than HHC fibre (p ≤ 0.003). These results suggest that balanced soluble and insoluble fibre concentrates can improve piglet performance.

The Effect of Prebiotic Supplements on the Gastrointestinal Microbiota and Associated Health Parameters in Pigs

Establishing a balanced and diverse microbiota in the GIT of pigs is crucial for optimizing health and performance throughout the production cycle. The post-weaning period is a critical phase, as it is often associated with dysbiosis, intestinal dysfunction and poor performance. Traditionally, intestinal dysfunctions associated with weaning have been alleviated using antibiotics and/or antimicrobials. However, increasing concerns regarding the prevalence of antimicrobial-resistant bacteria has prompted an industry-wide drive towards identifying natural sustainable dietary alternatives. Modulating the microbiota through dietary intervention can improve animal health by increasing the production of health-promoting metabolites associated with the improved microbiota, while limiting the establishment and proliferation of pathogenic bacteria. Prebiotics are a class of bioactive compounds that resist digestion by gastrointestinal enzymes, but which can still be utilized by beneficial microbes within the GIT. Prebiotics are a substrate for these beneficial microbes and therefore enhance their proliferation and abundance, leading to the increased production of health-promoting metabolites and suppression of pathogenic proliferation in the GIT. There are a vast range of prebiotics, including carbohydrates such as non-digestible oligosaccharides, beta-glucans, resistant starch, and inulin. Furthermore, the definition of a prebiotic has recently expanded to include novel prebiotics such as peptides and amino acids. A novel class of -biotics, referred to as "stimbiotics", was recently suggested. This bioactive group has microbiota-modulating capabilities and promotes increases in short-chain fatty acid (SCFA) production in a disproportionally greater manner than if they were merely substrates for bacterial fermentation. The aim of this review is to characterize the different prebiotics, detail the current understating of stimbiotics, and outline how supplementation to pigs at different stages of development and production can potentially modulate the GIT microbiota and subsequently improve the health and performance of animals.

Novel ex vivo screening assay to preselect farm specific pre- and probiotics in pigs

A novel rapid ex vivo assay was developed as part of a concept to determine potential tailor-made combinations of pre- and probiotics for individual farms. Sow faecal slurries from 20 German pig farms were anaerobically incubated with pre- and probiotics or their combinations together with pathogenic strains that are of interest in pig production. Aliquots of these slurries were then incubated with media containing antibiotic mixtures allowing only growth of the specific pathogen. Growth was monitored and lag time was used to determine the residual fitness of the pathogenic strains. The background growth could be inhibited for an Escherichia coli- and a Clostridium difficile- but not for a Clostridium perfringens strain. The prebiotic fructo-oligosaccharides (FOS) and its combination with probiotics reduced the residual fitness of the E. coli strain in some farms. However, notable exceptions occurred in other farms where FOS increased the fitness of the E. coli strain. Generally, combinations of pre- and probiotics did not show additive effects on fitness for E. coli but displayed farm dependent differences. The effects of pre- and probiotics on the residual fitness of the C. difficile strain were less pronounced, but distinct differences between single application of prebiotics and their combination with probiotics were observed. It was concluded that the initial composition of the microbiota in the samples was more determinative for incubations with the C. difficile strain than for incubations with the E. coli strain, as the presumed fermentation of prebiotic products showed less influence on the fitness of the C. difficile strain. Farm dependent differences were pronounced for both pathogenic strains and therefore, this novel screening method offers a promising approach for pre-selecting pre- and probiotics for individual farms. However, evaluation of farm metadata (husbandry, feed, management) will be crucial in future studies to determine a tailor-made solution for combinations of pre- and probiotics for individual farms. Also, refinement of the ex vivo assay in terms of on-farm processing of samples and validation of unambiguous growth for pathogenic strains from individual farms should be addressed.

Pre-Weaning Inulin Supplementation Alters the Ileal Transcriptome in Pigs Regarding Lipid Metabolism

Prebiotics, such as inulin, are non-digestible compounds that stimulate the growth of beneficial microbiota, which results in improved gut and overall health. In this study, we were interested to see if, and how, the ileal transcriptome altered after inulin administration in the pre-weaning period in pigs. Seventy-two Piétrain–Landrace newborn piglets were divided into three groups: (a) a control (CON) group (n = 24), (b) an inulin (IN)-0.5 group (n = 24), and (c) an IN-0.75 group (n = 24). Inulin was provided as a solution and administered twice a day. At week 4, eight piglets per group, those closest to the average in body weight, were sacrificed, and ileal scrapings were collected and analyzed using 3′ mRNA massively parallel sequencing. Only minor differences were found, and three genes were differentially expressed between the CON and IN-0.5 group, at an FDR of 10%. All three genes were downregulated in the IN-0.5 group. When comparing the CON group with the IN-0.75 group, five genes were downregulated in the IN-0.75 group, including the three genes seen earlier as differentially expressed between CON and IN-0.5. No genes were found to be differential expressed between IN-0.5 and IN-0.75. Validation of a selection of these genes was done using qRT-PCR. Among the downregulated genes were Angiopoietin-like protein 4 (ANGPTL4), Aquaporin 7 (AQP7), and Apolipoprotein A1 (APOA1). Thus, although only a few genes were found to be differentially expressed, several of them were involved in lipid metabolism, belonging to the peroxisome proliferator-activated receptor (PPAR) signaling pathway and known to promote lipolysis. We, therefore, conclude that these lipid metabolism genes expressed in the ileum may play an important role when supplementing piglets with inulin early in life, before weaning.

Metatranscriptomic analysis of colonic microbiota's functional response to different dietary fibers in growing pigs

Background

Dietary fibers are widely considered to be beneficial to health as they produce nutrients through gut microbial fermentation while facilitating weight management and boosting gut health. To date, the gene expression profiles of the carbohydrate active enzymes (CAZymes) that respond to different types of fibers (raw potato starch, RPS; inulin, INU; pectin, PEC) in the gut microbes of pigs are not well understood. Therefore, we investigated the functional response of colonic microbiota to different dietary fibers in pigs through metatranscriptomic analysis.

Results

The results showed that the microbial composition and CAZyme structure of the three experimental groups changed significantly compared with the control group (CON). Based on a comparative analysis with the control diet, RPS increased the abundance of Parabacteroides, Ruminococcus, Faecalibacterium and Alloprevotella but decreased Sutterella; INU increased the relative abundance of Fusobacterium and Rhodococcus but decreased Bacillus; and PEC increased the relative abundance of the Streptococcus and Bacteroidetes groups but decreased Clostridium, Clostridioides, Intestinibacter, Gemmiger, Muribaculum and Vibrio. The gene expression of CAZymes GH8, GH14, GH24, GH38, GT14, GT31, GT77 and GT91 downregulated but that of GH77, GH97, GT3, GT10 and GT27 upregulated in the RPS diet group; the gene expression of AA4, AA7, GH14, GH15, GH24, GH26, GH27, GH38, GH101, GT26, GT27 and GT38 downregulated in the INU group; and the gene expression of PL4, AA1, GT32, GH18, GH37, GH101 and GH112 downregulated but that of CE14, AA3, AA12, GH5, GH102 and GH103 upregulated in the PEC group. Compared with the RPS and INU groups, the composition of colonic microbiota in the PEC group exhibited more diverse changes with the variation of CAZymes and Streptococcus as the main contributor to CBM61, which greatly promoted the digestion of pectin.

Conclusion

The results of this exploratory study provided a comprehensive overview of the effects of different fibers on nutrient digestibility, gut microbiota and CAZymes in pig colon, which will furnish new insights into the impacts of the use of dietary fibers on animal and human health.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00108-1.

Swine gut microbiota and its interaction with host nutrient metabolism

Gut microbiota is generally recognized to play a crucial role in maintaining host health and metabolism. The correlation among gut microbiota, glycolipid metabolism, and metabolic diseases has been well reviewed in humans. However, the interplay between gut microbiota and host metabolism in swine remains incompletely understood. Given the limitation in conducting human experiments and the high similarity between swine and humans in terms of anatomy, physiology, polyphagy, habits, and metabolism and in terms of the composition of gut microbiota, there is a pressing need to summarize the knowledge gained regarding swine gut microbiota, its interplay with host metabolism, and the underlying mechanisms. This review aimed to outline the bidirectional regulation between gut microbiota and nutrient metabolism in swine and to emphasize the action mechanisms underlying the complex microbiome-host crosstalk via the gut microbiota-gut-brain axis. Moreover, it highlights the new advances in knowledge of the diurnal rhythmicity of gut microbiota. A better understanding of these aspects can not only shed light on healthy and efficient pork production but also promote our knowledge on the associations between gut microbiota and the microbiome-host crosstalk mechanism. More importantly, knowledge on microbiota, host health and metabolism facilitates the development of a precise intervention therapy targeting the gut microbiota.

Physiological, antimicrobial, intestine morphological, and immunological effects of fructooligosaccharides in pigs

In pig nutrition, there are some periods when natural alternatives to antibiotics are more required, such as during suckling and weaning. Fructooligosaccharides (FOSs) are a group of prebiotics applied as feed ingredients in animal nutrition since their positive effects on growth performance, immunological parameters, intestinal microbiota, and gut morphology are reported. Accordingly, FOS may be candidate molecules to improve the mentioned properties in pigs. Previous studies defined FOS as inhibiting the activity of pathogens and increasing the colonization of beneficial bacteria in the gut, although metabolites of FOS decreased the intestinal pH value. Beneficial effects on digestive-enzyme activities and on protein digestion were determined in some studies. All of the three types of FOS (inulin, oligomeric fructans, and short-chain FOSs) promoted the microbial composition of the gut by increasing the colonizations of Lactobacillus, Bifidobacterium, and Prevotella genus. FOS also affected the immune response directly and indirectly and increased vaccine-specific IgA, serum IgG, and IgE levels. Moreover, FOS enhanced the activation of T cells and altered the secretions of some cytokines. Levels of vaccine-specific IgG could not be increased after FOS supplements. In most cases, FOS modified intestinal morphological parameters, such as longer villi, villus-height-to-crypt-depth ratio, and thicker mucosa, which could suggest better absorptive functions. Results are contradictory on growth performance, which might be influenced by the chemical structure, the duration, and the dose of FOS, so further studies are required. This review aims to gather information regarding immunological, antimicrobial, intestine morphological, and growth performance properties of fructooligosaccharides in pigs.

The Effect of Dietary Helianthus tuberosus L. on the Populations of Pig Faecal Bacteria and the Prevalence of Skatole

Simple Summary

The elimination of boar taint by a method other than surgical castration without anaesthesia is currently one of the main topics in pig research. Boar taint occurs in meat from some entire male pigs and is undesirable for sensitive consumers. Boar taint is mainly caused by skatole. Skatole is produced by the breakdown of proteins by intestinal bacteria and can be stored in meat and reduce its sensory quality (taste and odour). Boar taint can be reduced by a diet high in easily fermentable saccharides, such as Jerusalem artichoke (Helianthus tuberosus L.). These saccharides change the bacterial colonisation in the intestines and thus reduce the production of skatole. The aim of this study was to evaluate the effects of different levels of Jerusalem artichoke on performance, carcass composition and skatole and indole levels in adipose tissue and on microbiota in faecal samples. In the present study, Jerusalem artichoke had no negative effect on the growth performance or carcass value in male pigs. Moreover, Jerusalem artichoke led to decreased skatole levels in the adipose tissue, probably due to the decreased level of proteolytic bacteria, which cause a higher rate of skatole production in the gastrointestinal tract. It seems that a dietary concentration of 8.1% of Jerusalem artichoke fed 13 days before slaughter is a sufficient dose for decreasing the skatole levels to those of castrated males, and this approach could be an alternative to the surgical castration of male pigs.

Abstract

Jerusalem artichoke contains inulin polysaccharide, which has prebiotic effects and influences the microbiota of the digestive tract. The addition of Jerusalem artichoke in boar diets may decrease the content of skatole and indole, which are the main constituents of boar taint, and may also negatively affect the taste and odor. The objective of this study was to evaluate the effects of different levels of Helianthus tuberosus L. (H. tuberosus) in feed mixtures on performance, carcass composition, the levels of microbiota in faecal samples, and the concentrations of skatole and indole in adipose tissue. The study was performed with 47 crossbred entire male pigs of the Large White _sire × (Large White _dame × Landrace) genotype fed a basal diet with 0%, 4.1%, 8.1% or 12.2% H. tuberosus for 13 days before slaughter. Significant differences in daily weight gain and daily feed intake were found (p = 0.045), with the values being lower in the group with the highest level of H. tuberosus. In addition, increasing levels of H. tuberosus decreased the concentration of skatole in the adipose tissue (p = 0.003). The highest level of H. tuberosus decreased the level of Escherichia coli (p ≤ 0.001) in the faeces. The enterococcal count increased (p = 0.029) in groups with a diet that included 4.1% and 8.1% H. tuberosus. There was also a significant correlation between the concentration of H. tuberosus and the concentration of E. coli (p < 0.001; −0.64) and the skatole levels in the adipose tissue (p = 0.001; –0.46). Moreover, there was also a positive correlation between the concentration of E. coli and the skatole levels in the adipose tissue (p = 0.023; 0.33). In conclusion, feeding pigs with H. tuberosus leads to decreased levels of skatole in the adipose tissue. According to the results of our study, a diet with 8.1% H. tuberosus is sufficient for decreasing skatole levels, which could be due to the decreased levels of pathogenic bacteria in the intestines.

Development of Salmonellosis as Affected by Bioactive Food Compounds

Infections caused by Salmonella serovars are the leading cause of foodborne hospitalizations and deaths in Americans, extensively prevalent worldwide, and pose a considerable financial burden on public health infrastructure and private manufacturing. While a comprehensive review is lacking for delineating the role of dietary components on prevention of Salmonellosis, evidence for the role of diet for preventing the infection and management of Salmonellosis symptoms is increasing. The current study is an evaluation of preclinical and clinical studies and their underlying mechanisms to elaborate the efficacy of bioactive dietary components for augmenting the prevention of Salmonella infection. Studies investigating dietary components such as fibers, fatty acids, amino acids, vitamins, minerals, phenolic compounds, and probiotics exhibited efficacy of dietary compounds against Salmonellosis through manipulation of host bile acids, mucin, epithelial barrier, innate and adaptive immunity and gut microbiota as well as impacting the cellular signaling cascades of the pathogen. Pre-clinical studies investigating synergism and/or antagonistic activities of various bioactive compounds, additional randomized clinical trials, if not curtailed by lack of equipoise and ethical concerns, and well-planned epidemiological studies could augment the development of a validated and evidence-based guideline for mitigating the public health burden of human Salmonellosis through dietary compounds.

The Mode of Action of Chicory Roots on Skatole Production in Entire Male Pigs Is neither via Reducing the Population of Skatole-Producing Bacteria nor via Increased Butyrate Production in the Hindgut

The effect of high levels of dietary chicory roots (25%) and intracecal exogenous butyrate infusion on skatole formation and gut microbiota was investigated in order to clarify the mechanisms underlying the known reducing effect of chicory roots on skatole production in entire male pigs. A Latin square design with 3 treatments (control, chicory, and butyrate), 3 periods, and 6 animals was carried out. Chicory roots showed the lowest numerical levels of skatole in both feces and plasma and butyrate infusion the highest. In the chicory group, an increased abundance of the skatole-producing bacterium Olsenella scatoligenes compared to the control group (P = 0.06), and a numerically higher relative abundance of Olsenella than for the control and butyrate groups, was observed. Regarding butyrate-producing bacteria, the chicory group had lower abundance of Roseburia but a numerically higher abundance of Megasphaera than the control group. Lower species richness was found in the chicory group than in the butyrate group. Moreover, beta diversity revealed that the chicory group formed a distinct cluster, whereas the control and butyrate groups clustered more closely to each other. The current data indicated that the skatole-reducing effect of chicory roots is neither via inhibition of cell apoptosis by butyrate nor via suppression of skatole-producing bacteria in the pig hindgut. Thus, the mode of action is most likely through increased microbial activity with a corresponding high incorporation of amino acids into bacterial biomass, and thereby suppressed conversion of tryptophan into skatole, as indicated in the literature.IMPORTANCE Castration is practiced to avoid the development of boar taint, which negatively affects the taste and odor of pork, and undesirable aggressive behavior. Due to animal welfare issues, alternatives to surgical castration are sought, though. Boar taint is a result of high concentrations of skatole and androstenone in back fat. Skatole is produced by microbial fermentation in the large intestine, and therefore, its production can be influenced by manipulation of the microbiota. Highly fermentable dietary fiber reduces skatole production. However, various theories have been proposed to explain the mode of action. In order to search for other alternatives, more efficient or less expensive, to reduce skatole via feeding, it is important to elucidate the mechanism behind the observed effect of highly fermentable dietary fiber on skatole. Our results indicate that highly fermentable dietary fiber does not affect skatole production by reducing the number of skatole-producing bacteria or stimulating butyrate production in the large intestine.

Effects of inulin supplementation to piglets in the suckling period on growth performance, postileal microbial and immunological traits in the suckling period and three weeks after weaning

The aim of this study was to investigate the effect of inulin (IN) supplementation to suckling piglets at and 3 weeks post-weaning. A total of 72 newborn piglets were used. Twenty-four piglets per group received different amounts of IN during the suckling period: (a) CON: no IN; (b) IN-0.5: 0.5 g IN/d on the 1st week, 1 g IN/d on the 2nd week, 1.5 g IN/d on the 3rd week and 2 g IN/d on the 4th week, or (c) IN-0.75: 0.75 g IN/d on the 1st week, 1.5 g IN/d on the 2nd week, 2.25 g IN/d on the 3rd week and 3 g IN/d on the 4th week. Starting at 28 d of age, piglets were weaned and received a post-weaning diet without inulin during the following 3 weeks. At both 28 d and 49 d of age, piglets were euthanised for sampling. Piglets of group IN-0.5 had the highest body weight starting from the 3rd week (p < 0.05), concomitant with the highest villus height and the ratio of villus height/crypt depth in the jejunum and ileum on both sampling days (p < 0.05). At 28 d of age, an increased concentration of propionate, iso-butyrate or total short chain fatty acids was observed between treatment IN-0.5 and the other groups in the caecum or colon (p < 0.05). Moreover, the relative abundance of Escherichia coli (p = 0.05) and Enterobacteriaceae (p = 0.01) in colonic digesta were reduced in IN-0.5-treated piglets, and in both IN-supplemented groups, colonic interleukin-8, tumor necrosis factor-α and toll-like receptor-4 mRNA abundance were decreased compared to the CON group (p < 0.05). However, at 49 d of age, most of these differences disappeared. In conclusion, treatment IN-0.5 improved during the suckling period of piglets development of intestine, but these beneficial effects were not lasting after weaning, when IN supplementation was terminated. Treatment IN-0.75, however, did not display a prebiotic effect.

Influence of different inclusion levels and chain length of inulin on microbial ecology and the state of mucosal protective barrier in the large intestine of young pigs

The objective of the study was to examine the effect of inulin level, in regard to its degree of polymerisation (DP), on microbial activity and mucosal immune system of the large intestine of pigs. A total of 56 castrated male piglets (PIC × Penarlan P76) were allocated to seven groups and fed from the 10th day of life cereal-based diets without the addition of inulin or with 1%, 2% or 3% of inulin with an average DP of 10 (IN10) or 23 (IN23). Pigs were sacrificed at the age of 50 days. Feeding IN10 diets increased fructan concentration in the large intestine compared with IN23 diets, but did not affect microbial activity, except for digesta pH and mucinase activity in the middle colon, which were greater at the 1% level compared with the control group and other IN10 diets, respectively. The concentration of secretory immunoglobulin A in the caecum and middle colon was reduced by the 1% IN10 diet compared with the control group. Pigs fed the 2% IN23 diet had a higher butyric acid concentration in the caecum and proximal colon and greater isoacid concentrations in the middle and distal colon in comparison to the control. Dietary level of IN23 did not affect secretory immunoglobulin A concentration but the count of caecal intraepithelial lymphocytes was higher in pigs on the 1% IN23 diet than on the control diet. Neither IN10 nor IN23 diets affected populations of Bifidobacterium or Lactobacillus spp. In conclusion, the effects of inulin in the large intestine of pigs depended on dietary level and DP. IN23 increased short-chain fatty acid production at the 2% level and slightly activated mucosal immune status at the 1% level.

Microbial Ecology along the Gastrointestinal Tract

The ecosystem of the human gastrointestinal (GI) tract traverses a number of environmental, chemical, and physical conditions because it runs from the oral cavity to the anus. These differences in conditions along with food or other ingested substrates affect the composition and density of the microbiota as well as their functional roles by selecting those that are the most suitable for that environment. Previous studies have mostly focused on Bacteria, with the number of studies conducted on Archaea, Eukarya, and Viruses being limited despite their important roles in this ecosystem. Furthermore, due to the challenges associated with collecting samples directly from the inside of humans, many studies are still exploratory, with a primary focus on the composition of microbiomes. Thus, mechanistic studies to investigate functions are conducted using animal models. However, differences in physiology and microbiomes need to be clarified in order to aid in the translation of animal model findings into the context of humans. This review will highlight Bacteria, Archaea, Fungi, and Viruses, discuss differences along the GI tract of healthy humans, and perform comparisons with three common animal models: rats, mice, and pigs.

The effects of prebiotics on microbial dysbiosis, butyrate production and immunity in HIV-infected subjects

Altered interactions between the gut mucosa and bacteria during HIV infection seem to contribute to chronic immune dysfunction. A deeper understanding of how nutritional interventions could ameliorate gut dysbiosis is needed. Forty-four subjects, including 12 HIV⁺ viremic untreated (VU) patients, 23 antiretroviral therapy-treated (ART⁺) virally suppressed patients (15 immunological responders and 8 non-responders) and 9 HIV^- controls (HIV^-), were blindly randomized to receive either prebiotics (scGOS/lcFOS/glutamine) or placebo (34/10) over 6 weeks in this pilot study. We assessed fecal microbiota composition using deep 16S rRNA gene sequencing and several immunological and genetic markers involved in HIV immunopathogenesis. The short dietary supplementation attenuated HIV-associated dysbiosis, which was most apparent in VU individuals but less so in ART⁺ subjects, whose gut microbiota was found more resilient. This compositional shift was not observed in the placebo arm. Significantly, declines in indirect markers of bacterial translocation and T-cell activation, improvement of thymic output, and changes in butyrate production were observed. Increases in the abundance of Faecalibacterium and Lachnospira strongly correlated with moderate but significant increases of butyrate production and amelioration of the inflammatory biomarkers soluble CD14 and high-sensitivity C-reactive protein, especially among VU. Hence, the bacterial butyrate synthesis pathway holds promise as a viable target for interventions.

Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations

BACKGROUND

Dietary fibers contribute to health and physiology primarily via the fermentative actions of the host's gut microbiome. Physicochemical properties such as solubility, fermentability, viscosity, and gel-forming ability differ among fiber types and are known to affect metabolism. However, few studies have focused on how they influence the gut microbiome and how these interactions influence host health. The aim of this study is to investigate how the gut microbiome of growing pigs responds to diets containing gel-forming alginate and fermentable resistant starch and to predict important interactions and functional changes within the microbiota.

RESULTS

Nine growing pigs (3-month-old), divided into three groups, were fed with either a control, alginate-, or resistant starch-containing diet (CON, ALG, or RS), and fecal samples were collected over a 12-week period. SSU (small subunit) rDNA amplicon sequencing data was annotated to assess the gut microbiome, whereas comprehensive microarray polymer profiling (CoMPP) of digested material was employed to evaluate feed degradation. Gut microbiome structure variation was greatest in pigs fed with resistant starch, where notable changes included the decrease in alpha diversity and increase in relative abundance of Lachnospiraceae- and Ruminococcus-affiliated phylotypes. Imputed function was predicted to vary significantly in pigs fed with resistant starch and to a much lesser extent with alginate; however, the key pathways involving degradation of starch and other plant polysaccharides were predicted to be unaffected. The change in relative abundance levels of basal dietary components (plant cell wall polysaccharides and proteins) over time was also consistent irrespective of diet; however, correlations between the dietary components and phylotypes varied considerably in the different diets.

CONCLUSIONS

Resistant starch-containing diet exhibited the strongest structural variation compared to the alginate-containing diet. This variation gave rise to a microbiome that contains phylotypes affiliated with metabolically reputable taxonomic lineages. Despite the significant microbiome structural shifts that occurred from resistant starch-containing diet, functional redundancy is seemingly apparent with respect to the microbiome's capacity to degrade starch and other dietary polysaccharides, one of the key stages in digestion.

Dietary inulin affects the intestinal microbiota in sows and their suckling piglets

Background

Several studies have focused on the effects of dietary inulin on the intestinal microbiota of weaned piglets. In the present study, inulin was added to a diet for gestating and lactating sows, expecting not only effects on the faecal microbiota of sows, but also on the bacterial cell numbers in the gastrointestinal tract of their piglets during the suckling period. Sows were fed a diet without (n = 11) or with (n = 10) 3% inulin, and selected bacterial groups were determined in their faeces ante and post partum. Suckling piglets, 8 per group, were euthanised on day 10 after birth to analyse digesta samples of the gastrointestinal tract.

Results

Dietary inulin increased the cell numbers of enterococci, both, in the faeces of the sows during gestation and lactation, and in the caecum of the piglets (P ≤ 0.05). Moreover, higher cell numbers of eubacteria (stomach) and C. leptum (caecum), but lower cell numbers of enterobacteria and L. amylovorus (stomach) were detected in the digesta of the piglets in the inulin group (P ≤ 0.05).

Conclusions

In conclusion, inulin seems to have the potential to influence the gastrointestinal microbiota of suckling piglets through the diet of their mother, showing the importance of the mother-piglet couple for the microbial development. Early modulation of the intestinal microbiota could be especially interesting with regard to the critical weaning time.

Impact of a probiotic, inulin, or their combination on the piglets' microbiota at different intestinal locations

Natural feed additives are used to maintain health and to promote performance of pigs without antibiotics. Effects of a probiotic, inulin, and their combination (synbiotic), on the microbial diversity and composition at different intestinal locations were analysed using denaturing gradient gel electrophoresis (DGGE), real-time PCR, and 16S rRNA gene pyrosequencing. Bacterial diversity assessed by DGGE and/or pyrosequencing was increased by inulin in all three gut locations and by the synbiotic in the caecum and colon. In contrast, the probiotic did only affect the microbiota diversity in the ileum. Shifts in the DGGE microbiota profiles of the caecum and colon were detected for the pro- and synbiotic fed animals, whereas inulin profiles were more similar to the ones of the control. 16S rRNA gene pyrosequencing revealed that all three additives could reduce Escherichia species in each gut location, indicating a potential beneficial effect on the gut microbiota. An increase of relative abundance of Clostridiaceae in the large intestine was found in the inulin group and of Enterococcaceae in the ileum of probiotic fed pigs. Furthermore, real-time PCR results showed that the probiotic and synbiotic increased bifidobacterial numbers in the ileum, which was supported by sequencing results. The probiotic and inulin, to different extents, changed the diversity, relative abundance of phylotypes, and community profiles of the porcine microbiota. However, alterations of the bacterial community were not uniformly between gut locations, demonstrating that functionality of feed additives is site specific. Therefore, gut sampling from various locations is crucial when investigations aim to identify the composition of a healthy gut microbiota after its manipulation through feed additives.

Dietary fibre and crude protein: impact on gastrointestinal microbial fermentation characteristics and host response

The role of the gastrointestinal tract microbiota in animal health and nutrition has become the subject of intensive research. Carbohydrates and crude protein are major components of swine diets and numerous studies have been performed looking at the effect of inclusion of dietary fibre with possible functional properties. In recent years, our understanding of the diversity and functionality of the gastrointestinal tract microbiota has increased further enabling the possibility for their targeted modulation. However, favouring potential beneficial bacteria, inhibiting possible pathogens or promotion of the formation of desired metabolites, is complex and underlies many factors and uncertainties. Approaches targeting this complex ecosystem (and discussed in this review) include the utilisation of fermentable carbohydrates such as resistant starch, cereal 1–3/1–4 β-glucans, arabinoxylans, inulin or other sources from legumes and industrial by-products. In addition, strategies regarding protein level and the protein : carbohydrate ratio are discussed briefly. Results are both promising and sometimes rather disillusioning considering the dietary concentrations needed to show biologically relevant effects. Deriving recommendations for an optimal inclusion rate of dietary fibre for weaning, growing pigs and sows and maximum levels for dietary crude protein may be one of the main challenges in the near future in the swine industry.

Differences in carbon source utilisation distinguish Campylobacter jejuni from Campylobacter coli

BACKGROUND

Campylobacter jejuni and C. coli are human intestinal pathogens that are the most frequent causes of bacterial foodborne gastroenteritis in humans in the UK. In this study, we aimed to characterise the metabolic diversity of both C. jejuni and C. coli using a diverse panel of clinical strains isolated from the UK, Pakistan and Thailand, thereby representing both the developed and developing world. Our aim was to apply multi genome analysis and Biolog phenotyping to determine differences in carbon source utilisation by C. jejuni and C. coli strains.

RESULTS

We have identified a core set of carbon sources (utilised by all strains tested) and a set that are differentially utilised for a diverse panel of thirteen C. jejuni and two C. coli strains. This study used multi genome analysis to show that propionic acid is utilised only by C. coli strains tested. A broader PCR screen of 16 C. coli strains and 42 C. jejuni confirmed the absence of the genes needed for propanoate metabolism.

CONCLUSIONS

From our analysis we have identified a phenotypic method and two genotypic methods based on propionic utilisation that might be applicable for distinguishing between C. jejuni and C. coli.

Intestinal concentrations of free and encapsulated dietary medium-chain fatty acids and effects on gastric microbial ecology and bacterial metabolic products in the digestive tract of piglets

The influence of low dietary levels of free and encapsulated medium-chain fatty acids on their concentrations in the digesta, the gastric microbial ecology and bacterial metabolic products in the gastrointestinal tract (GIT) in weaned piglets was studied. Starting after weaning, 36 piglets were fed a diet without (Control) or with medium-chain fatty acids uncoated (MCFA) or coated with vegetable fat and lecithin (MCFAc). After 4 weeks, the animals were killed, and digesta from the stomach and different sections of the GIT were collected. The concentrations of caprylic (p < 0.001) and capric (p = 0.001) acids were higher in the stomachs of piglets fed diets MCFA and MCFAc compared to the Control group. The concentrations dropped rapidly along the GIT, regardless of encapsulation, and tended to be higher in groups MCFA and MCFAc compared to the Control. Compared to the Control group, ingestion of diet MCFAc led to an increase in the number of eubacteria (p = 0.001), enterobacteriaceae (p < 0.001), clostridial clusters I (p = 0.001) and IV (p = 0.019), Lactobacillus johnsonii (p < 0.001) and Lactobacillus amylovorus (p = 0.001) in gastric contents. A similar trend was seen with diet MCFA. Relative concentrations of short-chain fatty acids were characterised by lower propionic acid levels (p = 0.045), numerically (p < 0.1) higher acetic, lower n-butyric and i-valeric acid concentrations in the small intestine. Lactic acid concentrations were not significantly changed in the GIT, but ammonia concentrations increased (p < 0.001) in the distal small intestine in the MCFA and MCFAc groups. In conclusion, medium-chain fatty acids affected microbial ecology parameters in the gastric contents and bacterial metabolites in the small intestine. At low dietary levels, medium-chain fatty acids may be regarded as modulators of the gastric microbiota in weaned piglets.

Dietary oligosaccharides increase colonic weight and the amount but not concentration of bacterially synthesized folate in the colon of piglets

Recently, we demonstrated that the large pool of folate present in the colon of humans can be absorbed. Here, we investigated whether the net amount of folate synthesized by bacteria in the colon of piglets can be modified by feeding prebiotics to alter their microbial milieu. Male piglets (age 5 d, n = 12) were randomized to a milk-based formula containing either 5 g/L inulin + 5 g/L galactooligosaccharides (IN-GOS) or 5 g/L maltodextrin (control). Body weight did not differ between groups during the 28-d feeding intervention. However, the mean weight of colonic tissue (38%) and their contents (238%) was higher in the IN-GOS than in the control group (P = 0.004, P = 0.0001, respectively). Total bacterial load in the colon of piglets fed IN-GOS was 531% greater and the total amount of folate found in the colon contents was 53% greater than that of controls (P = 0.002, P = 0.02, respectively). Indices of blood folate status (plasma and RBC folate and plasma homocysteine) and folate concentrations in liver and kidneys were unaffected. Both groups exhibited low RBC folate (56 ± 23 nmol/L) and elevated homocysteine (24 ± 7 μmol/L) concentrations, evidence of deficiency if present in humans. In conclusion, dietary supplementation with 5 g of inulin + 5 g of galactooligosaccharides increased the weight, bacterial load, and total folate content in the piglet colon; however, these changes were insufficient to modify indices of whole body folate status. Future studies investigating the impact of feeding prebiotics on localized folate status at the level of the colonocyte are warranted.

Inulin and probiotics in newly weaned piglets: effects on intestinal morphology, mRNA expression levels of inflammatory marker genes and haematology

The study aimed at determining the effect of inulin and/or a multispecies probiotic formulation on gastrointestinal tract (GIT) morphology, immunological and haematological parameters. Forty-eight newly weaned piglets were assigned to four feeding groups, receiving a standard basal diet (control), supplemented with 0.4% inulin, probiotics (1 x 10(9) CFU/kg as fed, enterococci, lactobacilli, bifidobacteria) or a combination of both (synbiotic). After four weeks of ad libitum feeding piglets were slaughtered and intestinal tissue samples were obtained for histometry. Additional tissue samples of the GIT, mesenteric lymph nodes, blood, liver and spleen were taken for mRNA expression analysis of cell turnover (CDK4, caspase3, IGF I), transcription factor NFkappaB and inflammatory marker genes (TNFalpha, TGFbeta). Changes in histometry occurred predominantly in the small intestine, showing higher jejunal villi when probiotics were administered alone (p < 0.10). Inulin decreased the number of acidic goblet cells in jejunal villi (p < 0.05), whereas probiotics increased neutral goblet cells in ileal villi (p < 0.05). Though inflammatory marker genes were uninfluenced by treatment in the proximal GIT, the colon showed downregulations induced by inulin (TNFalpha: p < 0.10, TGFbeta: p < 0.05). Gene expression of CDK4 was upregulated in the jejunum and of TGFbeta in the mesenteric lymph nodes in the probiotic groups. Interestingly, the probiotic group alone exhibited upregulations in cell turnover marker genes in the colon and blood. Furthermore, for numerous parameters, inulin and probiotics led to no synergistic but antagonistic interactions.

Impact of inulin and a multispecies probiotic formulation on performance, microbial ecology and concomitant fermentation patterns in newly weaned piglets

The effect of inulin and a multispecies probiotic formulation on performance and microbial parameters in a 28 days feeding trial with newly weaned piglets was assessed. Forty-eight piglets were allocated to a 2 × 2 factorial experiment involving two levels of inulin supplementation (0% or 0.4%) and two levels of probiotics (0 or 1 × 10(9) CFU/kg as fed, comprising enterococci, lactobacilli and bifidobacteria). In digesta samples obtained at slaughter (stomach, jejunum, ileum and colon), selected bacterial groups were enumerated and lactic acid, short chain fatty acids and ammonia concentrations analysed. The overall performance of piglets was unaffected by treatment. Inulin increased total aerobes in stomach and jejunum (p < 0.05), whereas enterococci declined in colon of the inulin group (p < 0.05). Furthermore decreasing colonic acetic acid (p < 0.01) and increasing lactic acid (p < 0.05) was observed for inulin. Probiotics increased total aerobes (p < 0.05) and enterococci (p < 0.01) in ileum and lactobacilli (p < 0.05), enterococci and gram-negative anaerobes (p < 0.01) in colon. Moreover, dry matter content in stomach and colon was lower and acetic acid in colon increased (p < 0.05). A decrease in ileal pH value was noted symbiotically for both additives. However, several parameters showed no synbiotic, but distinct individual effects of inulin and probiotics. Effects occurred along the entire gastrointestinal tract without restriction to the colon.

Nutritional programming of gastrointestinal tract development. Is the pig a good model for man?

The consequences of early-life nutritional programming in man and other mammalian species have been studied chiefly at the metabolic level. Very few studies, if any, have been performed in the gastrointestinal tract (GIT) as the target organ, but extensive GIT studies are needed since the GIT plays a key role in nutrient supply and has an impact on functions of the entire organism. The possible deleterious effects of nutritional programming at the metabolic level were discovered following epidemiological studies in human subjects, and confirmed in animal models. Investigating the impact of programming on GIT structure and function would need appropriate animal models due to ethical restrictions in the use of human subjects. The aim of the present review is to discuss the use of pigs as an animal model as a compromise between ethically acceptable animal studies and the requirement of data which can be interpolated to the human situation. In nutritional programming studies, rodents are the most frequently used model for man, but GIT development and digestive function in rodents are considerably different from those in man. In that aspect, the pig GIT is much closer to the human than that of rodents. The swine species is closely comparable with man in many nutritional and digestive aspects, and thus provides ample opportunity to be used in investigations on the consequences of nutritional programming for the GIT. In particular, the 'sow-piglets' dyad could be a useful tool to simulate the 'human mother-infant' dyad in studies which examine short-, middle- and long-term effects and is suggested as the reference model.