Prediction of nutrient digestibility in grower-finisher pigs based on faecal microbiota composition.

Microbiota play an important role in total tract nutrient digestion, especially when fibrous diets are fed to pigs. This study aimed to use metagenomics to predict faecal nutrient digestibility in grower-finisher pigs. The study design consisted of 160 three-way crossbreed grower-finisher pigs (80 female and 80 male) which were either fed a diet based on corn/soybean meal or a more fibrous diet based on wheat/barley/by-products. On the day before slaughter, faecal samples were collected and used to determine faecal digestibility of dry matter, ash, organic matter, crude protein, crude fat, crude fibre and non-starch polysaccharides. The faecal samples were also sequenced for the 16S hypervariable region of bacteria (V3/V4) to profile the faecal microbiome. With these data, we calculated the between-animal variation in faecal nutrient digestibility associated with variation in the faecal microbiome, that is the "microbiability". The microbiability values were significantly greater than zero for dry matter, organic matter, crude protein, crude fibre and non-starch polysaccharides, ranging from 0.58 to 0.93, as well as for crude fat with a value of 0.37, but not significantly different from zero for ash. Using leave-one-out cross-validation, we estimated the accuracy of predicting digestibility values of individual pigs based on their faecal microbiota composition. The accuracies of prediction for crude fat and ash digestibility were virtually 0, and for the other nutrients, the accuracies ranged from 0.42 to 0.63. In conclusion, the faecal microbiota composition gave high microbiability values for faecal digestibility of dry matter, organic matter, crude protein, crude fibre and non-starch polysaccharides. The accuracies of prediction are relatively low if the interest is in precisely predicting faecal nutrient digestibility of individual pigs, but are promising from the perspective of ranking animals in a genetic selection context.

Increasing intake of dietary soluble nutrients affects digesta passage rate in the stomach of growing pigs.

The passage rate of solids and liquids through the gastrointestinal tract differs. Increased dietary nutrient solubility causes nutrients to shift from the solid to the liquid digesta fraction and potentially affect digesta passage kinetics. We quantified: (1) the effect of three levels of dietary nutrient solubility (8, 19 and 31 % of soluble protein and sucrose in the diet) at high feed intake level (S) and (2) the effect of low v. high feed intake level (F), on digesta passage kinetics in forty male growing pigs. The mean retention time (MRT) of solids and liquids in the stomach and small intestine was assessed using TiO2 and Cr-EDTA, respectively. In addition, physicochemical properties of digesta were evaluated. Overall, solids were retained longer than liquids in the stomach (2·0 h, P<0·0001) and stomach+small intestine (1·6 h, P<0·001). When S increased, MRT in stomach decreased by 1·3 h for solids (P=0·01) and 0·7 h for liquids (P=0·002) but only at the highest level of S. When F increased using low-soluble nutrients, MRT in stomach increased by 0·8 h for solids (P=0·041) and 0·7 h for liquids (P=0·0001). Dietary treatments did not affect water-binding capacity and viscosity of digesta. In the stomach of growing pigs, dietary nutrient solubility affects digesta MRT in a non-linear manner, while feed intake level increases digesta MRT depending on dietary nutrient solubility. Results can be used to improve predictions on the kinetics of nutrient passage and thereby of nutrient digestion and absorption in the gastrointestinal tract.

Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development.

BACKGROUND: Gut microbial colonization and development of immune competence are intertwined and are influenced by early-life nutritional, environmental, and management factors. Perturbation of the gut microbiome at young age affects the crosstalk between intestinal bacteria and host cells of the intestinal mucosa. RESULTS: We investigated the effect of a perturbation of the normal early life microbial colonization of the jejunum in 1-day old chickens. Perturbation was induced by administering 0.8 mg amoxicillin per bird per day) via the drinking water for a period of 24 h. Effects of the perturbation were measured by 16S rRNA profiling of the microbiome and whole genome gene expression analysis. In parallel to what has been observed for other animal species, we hypothesized that such an intervention may have negative impact on immune development. Trends were observed in changes of the composition and diversity of the microbiome when comparing antibiotic treated birds with their controls. in the jejunum, the expression of numerous genes changed, which potentially leads to changes in biological activities of the small intestinal mucosa. Validation of the predicted functional changes was performed by staining immune cells in the small intestinal mucosa and a reduction in the number of macrophage-like (KUL01+) cells was observed due to a direct or indirect effect of the antibiotic treatment. We provide evidence that a short, early life antibiotic treatment affects both the intestinal microbiota (temporarily) and mucosal gene expression over a period of 2 weeks. CONCLUSION: These results underscore the importance of early life microbial colonization of the gut in relation to immune development and the necessity to explore the capabilities of a variety of early life dietary and/or environmental factors to modulate the programming for immune competence in broilers.

Dietary Amino Acid Deficiency Reduces the Utilization of Amino Acids for Growth in Growing Pigs after a Period of Poor Health.

BACKGROUND: During immune system activation, partitioning of amino acids (AAs) changes between protein gain and use by the immune system. OBJECTIVE: We determined the effects of health status and dietary AA deficiency on nitrogen retention and AA utilization in pigs. METHODS: Barrows (55 d of age) were obtained from good health (GH, n = 14) or poor health (PH, n = 14) status farms and allocated to a diet either adequate in essential amino acids (Adq) or 25% deficient in Met + Cys, Thr, and Trp (Def). Nitrogen balance was measured and AA irreversible loss rates (ILRs) were measured after an intravenous bolus of U-(13)C-labeled L-AAs. RESULTS: On arrival at the experimental facilities, the PH pigs had 14% lower serum albumin and 50% greater serum haptoglobin and blood leukocyte counts than the GH pigs (P < 0.01), but the PH pigs showed signs of recovery during the trial. Total tract nitrogen digestibility was 3 percentage points lower in the PH pigs (P < 0.01). The PH-Adq pigs had compensatory body weight gain after arrival, coinciding with 7% greater nitrogen retention (P < 0.01) in the PH pigs than in the GH pigs. The PH pigs had a 24% greater ILR for Lys. Health status × diet interactions for Lys (P = 0.07), Val (P = 0.03), and Leu (P = 0.10) pool sizes and a greater urea pool size in the PH pigs (P = 0.01) support the observation that the increase in the ILR of Lys in the PH pigs was related to oxidation when feeding the Def diet, but to synthesis when feeding the Adq diet. Feeding Def diets increased monocyte counts by 30% (P < 0.01). CONCLUSIONS: This study illustrates how the competition for AAs between protein synthesis associated with immune system activation and body protein deposition is greater when the dietary supply of Met + Cys, Thr, and Trp is limited in pigs during and after a period of poor health.

Induced lung inflammation and dietary protein supply affect nitrogen retention and amino acid metabolism in growing pigs.

It is hypothesised that during immune system activation, there is a competition for amino acids (AA) between body protein deposition and immune system functioning. The aim of the present study was to quantify the effect of immune system activation on N retention and AA metabolism in growing pigs, depending on dietary protein supply. A total of sixteen barrows received an adequate (Ad) or restricted (Res) amount of dietary protein, and were challenged at day 0 with intravenous complete Freund's adjuvant (CFA). At days - 5, 3 and 8, an irreversible loss rate (ILR) of eight AA was determined. CFA successfully activated the immune system, as indicated by a 2- to 4-fold increase in serum concentrations of acute-phase proteins (APP). Pre-challenge C-reactive protein concentrations were lower (P< 0·05) and pre- and post-challenge albumin tended to be lower in Res-pigs. These findings indicate that a restricted protein supply can limit the acute-phase response. CFA increased urinary N losses (P= 0·04) and tended to reduce N retention in Ad-pigs, but not in Res-pigs (P= 0·07). The ILR for Val was lower (P= 0·05) at day 8 than at day 3 in the post-challenge period. The ILR of most AA, except for Trp, were strongly affected by dietary protein supply and positively correlated with N retention. The correlations between the ILR and APP indices were absent or negative, indicating that changes in AA utilisation for APP synthesis were either not substantial or more likely outweighed by a decrease in muscle protein synthesis during immune system activation in growing pigs.

Dietary supplementation of zinc oxide modulates intestinal functionality during the post-weaning period in clinically healthy piglets.

BACKGROUND: To improve our understanding of host and intestinal microbiome interaction, this research investigated the effects of a high-level zinc oxide in the diet as model intervention on the intestinal microbiome and small intestinal functionality in clinically healthy post-weaning piglets. In study 1, piglets received either a high concentration of zinc (Zn) as zinc oxide (ZnO, Zn, 2,690 mg/kg) or a low Zn concentration (100 mg/kg) in the diet during the post weaning period (d 14-23). The effects on the piglet's small intestinal microbiome and functionality of intestinal tissue were investigated. In study 2, the impact of timing of the dietary zinc intervention was investigated, i.e., between d 0-14 and/or d 14-23 post weaning, and the consecutive effects on the piglet's intestinal functionality, here referring to microbiota composition and diversity and gene expression profiles. RESULTS: Differences in the small intestinal functionality were observed during the post weaning period between piglets receiving a diet with a low or high concentration ZnO content. A shift in the microbiota composition in the small intestine was observed that could be characterized as a non-pathological change, where mainly the commensals inter-changed. In the immediate post weaning period, i.e., d 0-14, the highest number of differentially expressed genes (DEGs) in intestinal tissue were observed between animals receiving a diet with a low or high concentration ZnO content, i.e., 23 DEGs in jejunal tissue and 11 DEGs in ileal tissue. These genes are involved in biological processes related to immunity and inflammatory responses. For example, genes CD59 and REG3G were downregulated in the animals receiving a diet with a high concentration ZnO content compared to low ZnO content in both jejunum and ileum tissue. In the second study, a similar result was obtained regarding the expression of genes in intestinal tissue related to immune pathways when comparing piglets receiving a diet with a high concentration ZnO content compared to low ZnO content. CONCLUSIONS: Supplementing a diet with a pharmaceutical level of Zn as ZnO for clinically healthy post weaning piglets influences various aspects intestinal functionality, in particular in the first two weeks post-weaning. The model intervention increased both the alpha diversity of the intestinal microbiome and the expression of a limited number of genes linked to the local immune system in intestinal tissue. The effects do not seem related to a direct antimicrobial effect of ZnO.

Amino acid supplementation counteracts negative effects of low protein diets on tail biting in pigs more than extra environmental enrichment.

Low protein (LP) diets may increase the occurrence of damaging behaviours, like tail biting, in pigs. We investigated the effect of supplementing a LP diet with indispensable amino acids (IAA) or environmental enrichment on tail biting. Undocked pigs (n = 48 groups of 12) received either a normal protein diet (NP), a LP, LP with supplemented IAA (LP+), or LP diet with extra environmental enrichment (LP-E+) during the starter, grower, and finisher phase. Performance, activity, behaviour, and body damage were recorded. LP and LP-E+ had a lower feed intake, growth, and gain-to-feed ratio, and were more active than NP and LP+ pigs. LP-E+ pigs interacted most often with enrichment materials, followed by LP, LP+, and NP pigs. LP pigs showed more tail biting than all other groups during the starter phase and the finisher phase (tendency) compared to NP and LP+ pigs. Thus, LP-E+ only reduced tail biting in the starter phase, whereas LP+ tended to do so throughout. Tail damage was more severe in LP pigs than in NP and LP+, with LP-E+ in between. In conclusion, IAA supplementation was more effective than extra environmental enrichment in countering the negative effects of a low protein diet on tail biting in pigs.

Sanitary Conditions on the Farm Alters Fecal Metabolite Profile in Growing Pigs.

The aim of this study was to use fecal metabolite profiling to evaluate the effects of contrasting sanitary conditions and the associated subclinical health status of pigs. We analyzed fecal metabolite profiles by nuclear magnetic resonance (1H NMR) from pigs aged 14 and 22 weeks. Pigs kept under low and high sanitary conditions differed in fecal metabolites related to the degradation of dietary starch, metabolism of the gut microbiome, and degradation of components of animal (host) origin. The metabolites that differed significantly (FDR < 0.1) were from metabolic processes involved in either maintaining nutrient digestive capacity, including purine metabolism, energy metabolism, bile acid breakdown and recycling, or immune system metabolism. The results show that the fecal metabolite profiles reflect the sanitary conditions under which the pigs are kept. The fecal metabolite profiles closely resembled the profiles of metabolites found in the colon of pigs. Fecal valerate and kynurenic acid could potentially be used as "non-invasive" biomarkers of immune or inflammatory status that could form the basis for monitoring subclinical health status in pigs.

Local intestinal microbiota response and systemic effects of feeding black soldier fly larvae to replace soybean meal in growing pigs.

Black soldier fly (Hermetia illucens; BSF) larvae as dietary protein source have the ability to deliver nutrients and could possess functional properties that positively support animal productivity and health. More knowledge, however, is needed to assess the impact of feeding a BSF based diet on gut and animal health. Sixteen post-weaned male pigs were randomly assigned to two groups and fed for three weeks with iso-caloric and iso-proteinaceous experimental diets prepared with either soybean meal (SBM) as reference protein source or with BSF as single source of dietary protein. At the end of the trial, the pigs were sacrificed to collect relevant digesta, gut tissue and blood samples to study changes induced by the dietary treatments using ~ omics based analyses. Inclusion of BSF in the diet supports the development of the intestinal microbiome that could positively influence intestinal health. By amine metabolite analysis, we identified two metabolites i.e. sarcosine and methionine sulfoxide, in plasma that serve as markers for the ingestion of insect based ingredients. BSF seems to possess functional properties indicated by the appearance of alpha-aminobutyric acid and taurine in blood plasma of pigs that are known to induce health beneficial effects.

The effects of birth weight and estimated breeding value for protein deposition on nitrogen efficiency in growing pigs.

The effects of birth weight (BiW; low BiW [LBW] vs. high BiW [HBW]) and estimated breeding value (EBV) for protein deposition (low EBV [LBV] vs. high EBV [HBV]) on N retention, N efficiency, and concentrations of metabolites in plasma and urine related to N efficiency in growing pigs were studied. At an age of 14 wk, 10 LBW-LBV (BiW: 1.07 ± 0.09 [SD] kg; EBV: -2.52 ± 3.97 g/d, compared with an average crossbred pig with a protein deposition of 165 g/d), 10 LBW-HBV (BiW: 1.02 ± 0.13 kg; EBV: 10.47 ± 4.26 g/d), 10 HBW-LBV (BiW: 1.80 ± 0.13 kg; EBV: -2.15 ± 2.28 g/d), and 10 HBW-HBV (BiW: 1.80 ± 0.15 kg; EBV: 11.18 ± 3.68 g/d) male growing pigs were allotted to the experiment. The pigs were individually housed in metabolism cages and were subjected to an N balance study in two sequential periods of 5 d, after an 11-d dietary adaptation period. Pigs were assigned to a protein adequate (A) or protein restricted (R, 70% of A) regime in a change-over design. Pigs were fed 2.8 times the energy requirements for maintenance. Nontargeted metabolomics analyses were performed in urine and blood plasma samples. The N retention (in g/d) was higher in the HBW than in the LBW pigs (P < 0.001). The N retention (in g/[kg metabolic body weight (BW0.75) · d]) and N efficiency, however, were not affected by the BiW of the pigs. The N retention (P = 0.04) and N efficiency (P = 0.04) were higher in HBV than in LVB pigs on the A regime but were not affected by EBV in pigs on the R regime. Restricting the dietary protein supply with 30% decreased the N retention (P < 0.001) but increased the N efficiency (P = 0.003). Nontargeted metabolomics showed that a hexose, free amino acids (AA), and lysophosphatidylcholines were the most important metabolites in plasma for the discrimination between HBV and LBV pigs, whereas metabolites of microbial origin contributed to the discrimination between HBV and LBV pigs in urine. This study shows that BiW does not affect N efficiency in the later life of pigs. Nitrogen efficiency and N retention were higher in HBV than in LBV pigs on the A regime but similar in HBV and LBV pigs on the R regime. In precision feeding concepts aiming to further optimize protein and AA efficiency in pigs, the variation in EBV for protein deposition of pigs should be considered as a factor determining N retention, growth performance, and N efficiency.

Birth weight affects body protein retention but not nitrogen efficiency in the later life of pigs.

Exploring factors that might affect nitrogen (N) efficiency in pigs could support the development of precision feeding concepts. Therefore, an experiment was conducted to determine the effects of birth weight (BiW) on N retention, N efficiency, and concentrations of metabolites in plasma and urine related to N efficiency in male pigs of 14 wk of age. BiW of the low BiW (LBW) and high BiW (HBW) pigs was 1.11 ± 0.14 and 1.79 ± 0.12 kg, respectively. Twenty LBW and 20 HBW pigs were individually housed in metabolism cages and were subjected to an N balance study in two sequential periods of 5 d, after an 11-d adaptation period. Pigs were assigned to a protein adequate (A) or protein restricted (R, 70% of A) regime in a change-over design and fed restrictedly 2.8 times the energy requirements for maintenance. Nontargeted metabolomics analyses were performed in urine and blood plasma samples. The N retention in g/d was higher in the HBW than in the LBW pigs (P < 0.001). The N retention in g/(kg BW0.75·d) and N efficiency (= 100% × N retention / N intake), however, were not affected by BiW of the pigs. Moreover, fecal digestibility of N and urinary concentration of N and urea were not affected by BiW of the pigs. The concentration of insulin (P = 0.08) and insulin-like growth factor-1 (IGF-1;P = 0.05) in blood plasma was higher in HBW pigs, whereas the concentration of α-amino N tended to be lower in HBW pigs (P = 0.06). The LBW and HBW pigs could not be discriminated based on the plasma and urinary metabolites retrieved by nontargeted metabolomics. Restricting dietary protein supply decreased N retention (P < 0.001), N efficiency (P = 0.07), fecal N digestibility (P < 0.001), urinary concentration of N and urea (P < 0.001), and concentration of urea (P < 0.001), IGF-1 (P < 0.001), and α-amino N (P < 0.001) in blood plasma. The plasma and urinary metabolites differing between dietary protein regime were mostly amino acids (AA) or their derivatives, metabolites of the tricarboxylic acid cycle, and glucuronidated compounds, almost all being higher in the pigs fed the A regime. This study shows that BiW affects absolute N retention but does not affect N efficiency in growing pigs. Therefore, in precision feeding concepts, BiW of pigs should be considered as a factor determining protein deposition capacity but less as a trait determining N efficiency.

Sanitary Conditions Affect the Colonic Microbiome and the Colonic and Systemic Metabolome of Female Pigs.

Differences in sanitary conditions, as model to induce differences in subclinical immune stimulation, affect the growth performance and nutrient metabolism in pigs. The objective of the present study was to evaluate the colonic microbiota and the colonic and systemic metabolome of female pigs differing in health status induced by sanitary conditions. We analyzed blood and colon digesta metabolite profiles using Nuclear Magnetic Resonance (1H NMR) and Triple quadrupole mass spectrometry, as well as colonic microbiota profiles. 1H NMR is a quantitative metabolomics technique applicable to biological samples. Weaned piglets of 4 weeks of age were kept under high or low sanitary conditions for the first 9 weeks of life. The microbiota diversity in colon digesta was higher in pigs subjected to low sanitary conditions (n = 18 per treatment group). The abundance of 34 bacterial genera was higher in colon digesta of low sanitary condition pigs, while colon digesta of high sanitary status pigs showed a higher abundance for four bacterial groups including the Megasphaera genus (p < 0.003) involved in lactate fermentation. Metabolite profiles (n = 18 per treatment group) in blood were different between both groups of pigs. These different profiles suggested changes in general nutrient metabolism, and more specifically in amino acid metabolism. Moreover, differences in compounds related to the immune system and responses to stress were observed. Microbiome-specific metabolites in blood were also affected by sanitary status of the pigs. We conclude that the microbiome composition in colon and the systemic metabolite profiles are affected by sanitary conditions and related to suboptimal health. These data are useful for exploring further relationships between health, metabolic status and performance and for the identification of biomarkers related to health (indices) and performance.

Effects of undigested protein-rich ingredients on polarised small intestinal organoid monolayers.

ABSTRACT: Here, we describe the use of monolayers of intestinal epithelial cells derived from intestinal organoids and transcriptomics to investigate the direct effects of dietary protein sources on epithelial function. Mechanically dissociated 3D organoids of mouse duodenum were used to generate a polarized epithelium containing all cell types found in the tissue of origin. The organoid-derived cell monolayers were exposed to 4% (w/v) of 'undigested (non-hydrolysed)-soluble' fraction of protein sources used as feed ingredients [soybean meal (SBM) and casein], or alternative protein sources (spray dried plasma protein, and yellow meal worm), or controls for 6 h prior to RNA isolation and transcriptomics. All protein sources altered expression of unique biological processes in the epithelial cells. Exposure of intestinal organoids to SBM downregulated expression of retinol and retinoid metabolic processes as well as cholesterol and lipid biosynthetic pathways, consistent with the reported hypotriglyceridaemic effect of soy protein in vivo. These findings support the use of intestinal organoids as models to evaluate complex interactions between dietary ingredients and the intestinal epithelium and highlights some unique host effects of alternative protein sources in animal feed and potentially human food. GRAPHICAL ABSTRACT: Schematic representation of the study. 3-dimensional organoids were generated from mouse duodenum (1). The organoids were subsequently dissociated into single cells (2) and grown as 2-dimensional polarised monolayers (3). Polarized monolayers of organoid cells were exposed to different protein sources [CAS, SBM, SDPP, YMW, or medium control (MC)] for 6 h (4) and further processed for imaging (5) gene expression (6), and biochemical assays (7), to investigate the effects of undigested protein sources on the duodenal epithelium.

Patterns of community assembly in the developing chicken microbiome reveal rapid primary succession.

The fine-scale temporal dynamics of the chicken gut microbiome are unexplored, but thought to be critical for chicken health and productivity. Here, we monitored the fecal microbiome of healthy chickens on days 1-7, 10, 14, 21, 28, and 35 after hatching, and performed 16S rRNA amplicon sequencing in order to obtain a high-resolution census of the fecal microbiome over time. In the period studied, the fecal microbiomes of the developing chickens showed a linear-log increase in community richness and consistent shifts in community composition. Three successional stages were detected: the first stage was dominated by vertically transmitted or rapidly colonizing taxa including Streptococcus and Escherichia/Shigella; in the second stage beginning on day 4, these taxa were displaced by rapid-growing taxa including Lachnospiraceae and Ruminococcus-like species variants; and in the third stage, starting on day 10, slow-growing, specialist taxa including Candidatus Arthrobacter and Romboutsia were detected. The patterns of displacement and the previously reported ecological characteristics of many of the dominant taxa observed suggest that resource competition plays an important role in regulating successional dynamics in the developing chicken gut. We propose that the boundaries between successional stages (3-4 and 14-21 days after hatching) may be optimal times for microbiome interventions.

Molecular networks affected by neonatal microbial colonization in porcine jejunum, luminally perfused with enterotoxigenic Escherichia coli, F4ac fimbria or Lactobacillus amylovorus.

The development of an early complex gut microbiota may play an important role in the protection against intestinal dysbiosis later in life. The significance of the developed microbiota for gut barrier functionality upon interaction with pathogenic or beneficial bacteria is largely unknown. The transcriptome of differently perfused jejunal loops of 12 caesarian-derived pigs, neonatally associated with microbiota of different complexity, was studied. Piglets received pasteurized sow colostrum at birth (d0), a starter microbiota (Lactobacillus amylovorus (LAM), Clostridium glycolicum, and Parabacteroides) on d1-d3, and a placebo inoculant (simple association, SA) or an inoculant consisting of sow's diluted feces (complex association, CA) on d3-d4. On d 26-37, jejunal loops were perfused for 8 h with either enterotoxigenic Escherichia coli F4 (ETEC), purified F4 fimbriae, LAM or saline control (CTRL). Gene expression of each intestinal loop was analyzed by Affymetrix Porcine Gene 1.1_ST array strips. Gene Set Enrichment Analysis was performed on expression values. Compared to CTRL, 184 and 74; 2 and 139; 2 and 48 gene sets, were up- and down-regulated by ETEC, F4 and LAM, respectively. ETEC up-regulated networks related to inflammatory and immune responses, RNA processing, and mitosis. There was a limited overlap in up-regulated gene sets between ETEC and F4 fimbriae. LAM down-regulated genes related to inflammatory and immune responses, as well as to cellular compound metabolism. In CA pigs, 57 gene sets were up-regulated by CA, while 73 were down-regulated compared to SA. CA up-regulated gene sets related to lymphocyte modulation and to cellular defense in all loop perfusions. In CA pigs, compared to SA pigs, genes for chemokine and cytokine activity and for response to external stimuli were down-regulated in ETEC-perfused loops and up-regulated in CTRL. The results highlight the importance of the nature of neonatal microbial colonization in the response to microbial stimuli later in life.

Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex.

Dietary fiber content and composition affect microbial composition and activity in the gut, which in turn influence energetic contribution of fermentation products to the metabolic energy supply in pigs. This may affect feed efficiency (FE) in pigs. The present study investigated the relationship between the fecal microbial composition and FE in individual growing-finishing pigs. In addition, the effects of diet composition and sex on the fecal microbiome were studied. Fecal samples were collected of 154 grower-finisher pigs (3-way crossbreeds) the day before slaughter. Pigs were either fed a diet based on corn/soybean meal (CS) or a diet based on wheat/barley/by-products (WB). Fecal microbiome was characterized by 16S ribosomal DNA sequencing, clustered by operational taxonomic unit (OTU), and results were subjected to a discriminant approach combined with principal component analysis to discriminate diets, sexes, and FE extreme groups (10 high and 10 low FE pigs for each diet by sex-combination). Pigs on different diets and males vs. females had a very distinct fecal microbiome, needing only 2 OTU for diet (P = 0.020) and 18 OTU for sex (P = 0.040) to separate the groups. The 2 most important OTU for diet, and the most important OTU for sex, were taxonomically classified as the same bacterium. In pigs fed the CS diet, there was no significant association between FE and fecal microbiota composition based on OTU (P > 0.05), but in pigs fed the WB diet differences in FE were associated with 17 OTU in males (P = 0.018) and to 7 OTU in females (P = 0.010), with 3 OTU in common for both sexes. In conclusion, our results showed a diet and sex-dependent relationship between FE and the fecal microbial composition at slaughter weight in grower-finisher pigs.

The effects of starter microbiota and the early life feeding of medium chain triglycerides on the gastric transcriptome profile of 2- or 3-week-old cesarean delivered piglets.

BACKGROUND: The stomach is an underestimated key interface between the ingesta and the digestive system, affecting the digestion and playing an important role in several endocrine functions. The quality of starter microbiota and the early life feeding of medium chain triglycerides may affect porcine gastric maturation. Two trials (T1, T2) were carried out on 12 and 24 cesarean-delivered piglets (birth, d0), divided over two microbiota treatments, but slaughtered and sampled at two or three weeks of age, respectively. All piglets were fed orally: sow serum (T1) or pasteurized sow colostrum (T2) on d0; simple starter microbiota (Lactobacillus amylovorus, Clostridium glycolicum and Parabacteroides spp.) (d1-d3); complex microbiota inoculum (sow diluted feces, CA) or a placebo (simple association, SA) (d3-d4) and milk replacer ad libitum (d0-d4). The The T1 piglets and half of the T2 piglets were then fed a moist diet (CTRL); the remaining half of the T2 piglets were fed the CTRL diet fortified with medium chain triglycerides and 7% coconut oil (MCT). Total mRNA from the oxyntic mucosa was analyzed using Affymetrix©Porcine Gene array strips. Exploratory functional analysis of the resulting values was carried out using Gene Set Enrichment Analysis. RESULTS: Complex microbiota upregulated 11 gene sets in piglets of each age group vs. SA. Of these sets, 6 were upregulated at both ages, including the set of gene markers of oxyntic mucosa. In comparison with the piglets receiving SA, the CA enriched the genes in the sets related to interferon response when the CTRL diet was given while the same sets were impoverished by CA with the MCT diet. CONCLUSIONS: Early colonization with a complex starter microbiota promoted the functional maturation of the oxyntic mucosa in an age-dependent manner. The dietary fatty acid source may have affected the recruitment and the maturation of the immune cells, particularly when the piglets were early associated with a simplified starter microbiota.

A link between damaging behaviour in pigs, sanitary conditions, and dietary protein and amino acid supply.

The tendency to reduce crude protein (CP) levels in pig diets to increase protein efficiency may increase the occurrence of damaging behaviours such as ear and tail biting, particularly for pigs kept under suboptimal health conditions. We studied, in a 2×2×2 factorial design, 576 tail-docked growing-finishing entire male pigs in 64 pens, subjected to low (LSC) vs. high sanitary conditions (HSC), and fed a normal CP (NP) vs. a low CP diet (LP, 80% of NP) ad libitum, with a basal amino acid (AA) profile or supplemented AA profile with extra threonine, tryptophan and methionine. The HSC pigs were vaccinated in the first nine weeks of life and received antibiotics at arrival at experimental farm at ten weeks, after which they were kept in a disinfected part of the farm with a strict hygiene protocol. The LSC pigs were kept on the same farm in non-disinfected pens to which manure from another pig farm was introduced fortnightly. At 15, 18, and 24 weeks of age, prevalence of tail and ear damage and of tail and ear wounds was scored. At 20 and 23 weeks of age, frequencies of biting behaviour and aggression were scored for 10×10 min per pen per week. The prevalence of ear damage during the finisher phase (47 vs. 32% of pigs, P < 0.0001) and the frequency of ear biting (1.3 vs. 1.2 times per hour, P = 0.03) were increased in LSC compared with HSC pigs. This effect on ear biting was diet dependent, however, the supplemented AA profile reduced ear biting only in LSC pigs by 18% (SC × AA profile, P < 0.01). The prevalence of tail wounds was lower for pigs in LSC (13 ± 0.02) than for pigs in HSC (0.22 ± 0.03) in the grower phase (P < 0.007). Regardless of AA profile or sanitary status, LP pigs showed more ear biting (+20%, P < 0.05), tail biting (+25%, P < 0.10), belly nosing (+152%, P < 0.01), other oral manipulation directed at pen mates (+13%, P < 0.05), and aggression (+30%, P < 0.01) than NP pigs, with no effect on ear or tail damage. In conclusion, both low sanitary conditions and a reduction of dietary protein increase the occurrence of damaging behaviours in pigs and therefore may negatively impact pig welfare. Attention should be paid to the impact of dietary nutrient composition on pig behaviour and welfare, particularly when pigs are kept under suboptimal (sanitary) conditions.

Amine Metabolism Is Influenced by Dietary Protein Source.

Growth in world population will inevitably leads to increased demand for protein for humans and animals. Protein from insects and blood plasma are being considered as possible alternatives, but more research on their nutritional quality and health effects is needed. Here, we studied the effect of dietary protein source on metabolism and metabolic amine profiles in serum and urine of mice. Groups of mice were fed semi-purified diets containing 300 g/kg of soybean meal, casein, partially delactosed whey powder, spray-dried plasma protein, wheat gluten meal, and yellow mealworm. Feed and water intake as well as body weight gain were measured for 28 days. After 14 and 28 days, serum and urine samples were collected for measurement of a large panel of amine metabolites. MetaboAnalyst 3.0 was used for analysis of the raw metabolic data. Out of 68 targeted amine metabolites, we could detect 54 in urine and 41 in blood serum. Dietary protein sources were found to have profound effects on host metabolism, particularly in systemic amine profiles, considered here as an endophenotype. We recommend serum over urine to screen for the amine metabolic endophenotype based on partial least squares discriminant analysis. We concluded that metabolites like alpha-aminobutyric acid and 1-methylhistidine are sensitive indicators of too much or too little availability of specific amino acids in the different protein diets. Furthermore, we concluded that amine metabolic profiles can be useful for assessing the nutritional quality of different protein sources.