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Abstract Background Mixing pigs at weaning can compromise pig welfare and growth. Therefore, grouping littermates together may allow a diet nutrient and energy density reduction during the nursery period to reduce feed cost without affecting slaughter weight. This study investigated the combined effect of mixing and reducing dietary energy and nutrient density on growth performance, body lesions (BL), and behaviour in pigs from weaning to slaughter. Results Forty-eight litters [554 pigs, 11–12 pigs/litter; Danish Duroc × (Large White × Landrace)] were included in the trial. At 28 days of age, pigs were weaned and housed in nursery rooms in litter groups (INTACT, n = 24) or mixed with other litters and grouped by weight to reduce within-pen pig weight variation (MIXED, n = 24). A dietary regimen meeting pigs’ nutritional requirements (CON) and a low-density dietary regimen (LOW; -10% energy and protein) completed a 2 × 2 factorial arrangement (Mixing x Diet, n = 12). On day 74 of age, pigs moved to the grower-finisher accommodation without further mixing and all pigs received the CON dietary regimen. Mixing increased FCR by 4.0% during the nursery period (p = 0.003). Nursery pigs fed LOW experienced a growth retardation which was maintained until slaughter (-2.6 kg slaughter weight; p = 0.025). Initial differences in the coefficient of variation (CV) between MIXED (10.4%) and INTACT (17.6%; p

Abstract This study examined the effects of maternal and/or post-weaning Bacillus altitudinis supplementation on the microbiota in sow colostrum and faeces, and offspring digesta and faeces. Sows (n = 12/group) were assigned to: (1) standard diet (CON), or (2) CON supplemented with probiotic B. altitudinis spores (PRO) from day (d)100 of gestation to weaning (d26 of lactation). At weaning, offspring were assigned to CON or PRO for 28d, resulting in: (1) CON/CON, (2) CON/PRO, (3) PRO/CON, and (4) PRO/PRO, after which all received CON. Samples were collected from sows and selected offspring (n = 10/group) for 16S rRNA gene sequencing. Rothia was more abundant in PRO sow colostrum. Sow faeces were not impacted but differences were identified in offspring faeces and digesta. Most were in the ileal digesta between PRO/CON and CON/CON on d8 post-weaning; i.e. Bacteroidota, Alloprevotella, Prevotella, Prevotellaceae, Turicibacter, Catenibacterium and Blautia were more abundant in PRO/CON, with Firmicutes and Blautia more abundant in PRO/PRO compared with CON/CON. Lactobacillus was more abundant in PRO/CON faeces on d118 post-weaning. This increased abundance of polysaccharide-fermenters (Prevotella, Alloprevotella, Prevotellaceae), butyrate-producers (Blautia) and Lactobacillus likely contributed to previously reported improvements in growth performance. Overall, maternal, rather than post-weaning, probiotic supplementation had the greatest impact on intestinal microbiota.

Abstract Nisin is a broad spectrum bacteriocin used extensively as a food preservative that was identified in Lactococcus lactis nearly a century ago. We show that orally-ingested nisin survives transit through the porcine gastrointestinal tract intact (as evidenced by activity and molecular weight determination) where it impacts both the composition and functioning of the microbiota. Specifically, nisin treatment caused a reversible decrease in Gram positive bacteria, resulting in a reshaping of the Firmicutes and a corresponding relative increase in Gram negative Proteobacteria. These changes were mirrored by the modification in relative abundance of pathways involved in acetate, butyrate (decreased) and propionate (increased) synthesis which correlated with overall reductions in short chain fatty acid levels in stool. These reversible changes that occur as a result of nisin ingestion demonstrate the potential of bacteriocins like nisin to shape mammalian microbiomes and impact on the functionality of the community.

Antibiotics and zinc oxide restrictions encourage the search for alternatives to combat intestinal pathogens, including enterotoxigenic Escherichia coli (ETEC), a major cause of postweaning diarrhea (PWD) in pigs. PWD causes important economic losses for conventional and organic farming. This study investigated the effect of dietary supplementation with garlic and apple pomace or blackcurrant on infection indicators and the fecal microbiota of organic-raised piglets challenged with ETEC-F18. For 21 days, 32 piglets (7-weeks-old) were randomly assigned to one of four groups: non-challenge (NC); ETEC-challenged (PC); ETEC-challenged receiving garlic and apple pomace (3 + 3%; GA); ETEC-challenged receiving garlic and blackcurrant (3 + 3%; GB). ETEC-F18 was administered (8 mL; 109 CFU/ml) on days 1 and 2 postweaning. The 1st week, PC had lower average daily gain than those in the NC, GA, and GB groups (P < 0.05). NC pigs showed neither ETEC-F18 shedding nor signs of diarrhea. The PC group had higher diarrhea incidence and lower fecal dry matter than NC (≈5–10 days; 95% sEBCI). The GA and GB groups showed reduced ETEC-F18 and fedA gene shedding, higher fecal dry matter, and lower diarrhea incidence than the PC (≈5–9 days; 95% sEBCI). The NC, GA, and GB had normal hematology values during most of the study, whereas the PC had increased (P < 0.05) red blood cells, hemoglobin, and hematocrit on day 7. Haptoglobin and pig-MAP increased in all groups, peaking on day 7, but PC showed the greatest increase (P < 0.05). The fecal microbiota of PC pigs had reduced α-diversity (day 7; P < 0.05) and higher volatility (days 3–14; P < 0.05). Escherichia, Campylobacter, and Erysipelothrix were more abundant in the PC than in the NC, GB, and GA groups (log2FC > 2; P < 0.05), whereas Catenibacterium, Dialister, and Mitsoukella were more abundant in the NC, GB, and GA than in the PC group (log2FC > 2; P < 0.05). Prevotella and Lactobacillus were more abundant in the GB group (log2FC > 2, P < 0.05). In conclusion, dietary supplementation of GA and GB limited ETEC proliferation, reduced PWD, and beneficially impacted the fecal microbiota's diversity, composition, and stability.

Three Lactococcus lactis strains from the nasal microbiota of healthy pigs were identified as candidates for reducing MRSA in pigs. The safety of nasal administration of a cocktail of these strains was examined in new-born piglets. Six days pre-farrowing, twelve sows were assigned to the placebo or cocktail group (n = 6/group). After farrowing, piglets were administered with either 0.5 mL of the placebo or the cocktail to each nostril. Health status and body weight were monitored at regular time points. Two piglets from three sows/treatment group were euthanised at 24 h, 96 h and 14 d after birth, and conchae, lung and tonsil samples were collected for histopathological and gene expression analysis. Health scores were improved in the cocktail group between d1–5. Body weight and daily gains did not differ between groups. Both groups displayed histological indications of euthanasia and inflammation in the lungs, signifying the findings were not treatment related. The expression of pBD2, TLR9 and IL-1β in the nasal conchae differed between groups, indicating the cocktail has the potential to modulate immune responses. In summary, the L. lactis cocktail was well tolerated by piglets and there was no negative impact on health scores, growth or lung histopathology indicating that it is safe for administration to new-born piglets.

Abstract The objective was to evaluate the effect of dietary Bacillus altitudinis spore supplementation during day (D)0–28 post-weaning (PW) and/or D29–56 PW compared with antibiotic and zinc oxide (AB + ZnO) supplementation on pig growth and gut microbiota. Eighty piglets were selected at weaning and randomly assigned to one of five dietary treatments: (1) negative control (Con/Con); (2) probiotic spores from D29–56 PW (Con/Pro); (3) probiotic spores from D0–28 PW (Pro/Con); (4) probiotic spores from D0–56 PW (Pro/Pro) and (5) AB + ZnO from D0–28 PW. Overall, compared with the AB + ZnO group, the Pro/Con group had lower body weight, average daily gain and feed intake and the Pro/Pro group tended to have lower daily gain and feed intake. However, none of these parameters differed between any of the probiotic-treated groups and the Con/Con group. Overall, AB + ZnO-supplemented pigs had higher Bacteroidaceae and Prevotellaceae and lower Lactobacillaceae and Spirochaetaceae abundance compared to the Con/Con group, which may help to explain improvements in growth between D15–28 PW. The butyrate-producing genera Agathobacter, Faecalibacterium and Roseburia were more abundant in the Pro/Con group compared with the Con/Con group on D35 PW. Thus, whilst supplementation with B. altitudinis did not enhance pig growth performance, it did have a subtle, albeit potentially beneficial, impact on the intestinal microbiota.

Abstract Since the 1940s, Staphylococcus aureus has adapted to the use of different antimicrobials to treat infections. Although S. aureus can act as a commensal bacterium, some strains are facultative pathogens and acquiring them can be fatal. In particular, treating infections caused by S. aureus with acquired antimicrobial resistance is problematic, as their treatment is more difficult. Some of these S. aureus variants are methicillin-resistant S. aureus (MRSA) with prevalence across the globe in health-care facilities, community settings and on livestock farms. Apart from humans, MRSA can colonise other animal species, and because of this, resistance to new antimicrobials can appear and jump between species. Livestock and companion animals are particularly important in this regard considering the relatively high usage of antimicrobials in these species. There is a risk to humans who come into direct contact with animals acquiring MRSA but there is also the risk of animals acquiring MRSA from colonised humans. In this review, we summarise studies conducted worldwide to characterise the prevalence of MRSA in veterinarians, farmers and other personnel who come into close contact with animals. Finally, alternative treatment, preventive measures and on-farm strategies to reduce MRSA introduction to a farm and carriage within a herd are discussed.

Weaning is a critical period in a pig’s life. Piglets are confronted with abrupt changes to their physical and social environment, as well as management and nutritional changes. Weaning has always been associated with a growth check and is frequently accompanied by post-weaning diarrhoea in piglets. However, rapid increases in litter size in the last decade have increased within-litter piglet weight variation, with piglets now generally lighter at weaning, making the challenges associated with weaning even greater. Many interventions can be employed during the suckling period to ease the weaning transition for piglets. Pre-weaning strategies such as supervised farrowing (assistance with suckling and oxytocin provision), the provision of pain relief to sows around farrowing, split-suckling, early oral supplementation with glucose, bovine colostrum, faecal microbiota transplantation, feed additives and solid and liquid creep feeding (milk and liquid feed) have all been investigated. The objective of these strategies is to stimulate earlier maturation of the digestive tract, improve immunity, reduce latency to the first feed post-weaning and increase early post-weaning feed intake and growth. This review focuses in particular on: (1) pain relief provision to sows around farrowing, (2)split-suckling of piglets, (3) pre-weaning provision of supplementary milk and/or liquid feed, (4) other strategies to stimulate earlier enzyme production (e.g., enzyme supplementation), (5) other nutritional strategies to promote improved gut structure and function (e.g., L-glutamine supplementation), and (6) other strategies to modulate gut microbiota (e.g., probiotics and prebiotics). Correctly implementing these strategies can, not only increase post-weaning growth and reduce mortality, but also maximise lifetime growth in pigs.

Abstract Salmonella Typhimurium and its monophasic variant S. 4,[5],12:i:- are the dominant serotypes associated with pigs in many countries. We investigated their population structure on nine farms using whole genome sequencing, and their genotypic and phenotypic variation. The population structure revealed the presence of phylogenetically distinct clades consisting of closely related clones of S. Typhimurium or S. 4,[5],12:i:- on each pig farm, that persisted between production cycles. All the S. 4,[5],12:i:- strains carried the Salmonella genomic island-4 (SGI-4), which confers resistance to heavy metals, and half of the strains contained the mTmV prophage, harbouring the sopE virulence gene. Most clonal groups were highly drug resistant due to the presence of multiple antimicrobial resistance (AMR) genes, and two clades exhibited evidence of recent on-farm plasmid-mediated acquisition of additional AMR genes, including an IncHI2 plasmid. Biofilm formation was highly variable but had a strong phylogenetic signature. Strains capable of forming biofilm with the greatest biomass were from the S. 4,[5],12:i:- and S. Typhimurium DT104 clades, the two dominant pandemic clones found over the last 25 years. On-farm microevolution resulted in enhanced biofilm formation in subsequent production cycle.

Abstract Background With the increasing global population and increasing demand for food, the generation of food waste and animal manure increases. Anaerobic digestion is one of the best available technologies for food waste and pig manure management by producing methane-rich biogas. Dry co-digestion of food waste and pig manure can significantly reduce the reactor volume, capital cost, heating energy consumption and the cost of digestate liquid management. It is advantageous over mono-digestion of food waste or pig manure due to the balanced carbon/nitrogen ratio, high pH buffering capacity, and provision of trace elements. However, few studies have been carried out to study the roles of and interactions among microbes in dry anaerobic co-digestion systems. Therefore, this study aimed to assess the effects of different inocula (finished digestate and anaerobic sludge taken from wastewater treatment plants) and substrate compositions (food waste to pig manure ratios of 50:50 and 75:25 in terms of volatile solids) on the microbial community structure in food waste and pig manure dry co-digestion systems, and to examine the possible roles of the previously poorly described bacteria and the interactions among dry co-digestion-associated microbes. Results The dry co-digestion experiment lasted for 120 days. The microbial profile during different anaerobic digestion stages was explored using high-throughput 16S rRNA gene amplicon sequencing. It was found that the inoculum factor was more significant in determining the microbial community structure than the substrate composition factor. Significant correlation was observed between the relative abundance of specific microbial taxa and digesters’ physicochemical parameters. Hydrogenotrophic methanogens dominated in dry co-digestion systems. Conclusions The possible roles of specific microbial taxa were explored by correlation analysis, which were consistent with the literature. Based on this, the anaerobic digestion-associated roles of 11 bacteria, which were previously poorly understood, were estimated here for the first time. The inoculum played a more important role in determining the microbial community structure than substrate composition in dry co-digestion systems. Hydrogenotrophic methanogenesis was a significant methane production pathway in dry co-digestion systems.

Abstract Background Feed efficiency (FE) is an indicator of efficiency in converting energy and nutrients from feed into a tissue that is of major environmental and economic significance. The molecular mechanisms contributing to differences in FE are not fully elucidated, therefore the objective of this study was to profile the porcine Longissimus thoracis et lumborum (LTL) muscle transcriptome, examine the product quality from pigs divergent in FE and investigate the functional networks underpinning the potential relationship between product quality and FE. Results RNA-Seq (n = 16) and product quality (n = 40) analysis were carried out in the LTL of pigs differing in FE status. A total of 272 annotated genes were differentially expressed with a P < 0.01. Functional annotation revealed a number of biological events related to immune response, growth, carbohydrate & lipid metabolism and connective tissue indicating that these might be the key mechanisms governing differences in FE. Five most significant bio-functions altered in FE groups were ‘haematological system development & function’, ‘lymphoid tissue structure & development’, ‘tissue morphology’, ‘cellular movement’ and ‘immune cell trafficking’. Top significant canonical pathways represented among the differentially expressed genes included ‘IL-8 signalling’, ‘leukocyte extravasation signalling, ‘sphingosine-1-phosphate signalling’, ‘PKCθ signalling in T lymphocytes’ and ‘fMLP signalling in neutrophils’. A minor impairment in the quality of meat, in relation to texture and water-holding capacity, produced by high-FE pigs was observed. High-FE pigs also had reduced intramuscular fat content and improved nutritional profile in terms of fatty acid composition. Conclusions Ontology analysis revealed enhanced activity of adaptive immunity and phagocytes in high-FE pigs suggesting more efficient conserving of resources, which can be utilised for other important biological processes. Shifts in carbohydrate conversion into glucose in FE-divergent muscle may underpin the divergent evolution of pH profile in meat from the FE-groups. Moreover, altered amino acid metabolism and increased mobilisation & flux of calcium may influence growth in FE-divergent muscle. Furthermore, decreased degradation of fibroblasts in FE-divergent muscle could impact on collagen turnover and alter tenderness of meat, whilst enhanced lipid degradation in high-FE pigs may potentially underlie a more efficient fat metabolism in these animals.

There is evidence that spontaneous fermentation frequently occurs in liquid pig feed that is intended to be delivered as fresh liquid feed, often with a resultant deterioration in the microbial and nutritional quality of the feed, which can negatively affect pig health and growth. Strategies including controlled fermentation with microbial inoculants, pre-fermentation or soaking of the cereal fraction of the diet, enzyme supplementation and dietary acidification have been employed to inhibit pathogens and prevent deterioration of feed nutritional quality, with promising results obtained in many cases. This review evaluates the impact of these strategies on the microbial quality of liquid feed and discusses how they can be further improved. It also investigates if/how these strategies impact the pig gut microbiota and growth performance of liquid-fed pigs. Finally, we review liquid feed system sanitisation practices, which are highly variable from farm to farm and discuss the impact of these practices and whether they are beneficial or detrimental to liquid feed microbial quality. Overall, we provide a comprehensive review of the current state of knowledge on liquid feed for pigs, focusing on factors affecting microbial quality and strategies for its optimisation, as well as its impact on the pig gut microbiome.

The in-vitro ileal digestibility of dry matter (DM), organic matter (OM), and crude protein (CP) of field beans treated with propionic acid (trFB) and extruded trFB (exFB) was determined in experiment 1. The DE and dCP values of trFB and exFB were determined using the difference method in experiment 2. The effect of replacing SBM with trFB and exFB in grow-finisher diets on growth, carcass quality, apparent ileal digestibility (AiD), and total tract digestibility (ATTD) of DM, OM, gross energy (GE), and CP were investigated in experiment 3. In exp. 1, in-vitro digestibility of exFB compared to trFB was unchanged for DM (p = 0.12), increased for OM (p < 0.05), and increased for CP (p < 0.05). In exp. 2, the DE value of trFB and exFB was 14.38 and 15.75 MJ/kg respectively; and the dCP value was 21.35% and 21.42% respectively (on DM basis). In exp. 3, ADFI was higher for pigs fed trFB and exFB compared to the control diet (CON; p < 0.05), while ADG, FCR and carcass quality parameters of pigs did not differ among treatments (p > 0.05).

Gestational and early life experiences affect subsequent behavioural and physical development. The objective of the current study was to investigate associations between gilts’ fear of humans, gestational stress level, and feeding and maternal behaviour, as well as how these related to aspects of the personality and growth of their offspring. A total of 37 gilts were used. Four human approach tests were performed between d 104 and d 111 of gestation to classify gilts as fearful or friendly. Gilt feeding behaviour and salivary cortisol concentration was measured between d 90 and d 108 of gestation, and gilt nursing behaviour assessed at d 13 of lactation. Piglets were subject to a back test at d 13 of age, to an open field test and a human approach test at d 20 of age, and growth was monitored to weaning (d 26 of age). Gilts classified as having a fearful behavioural profile had higher cortisol levels than friendly gilts (p < 0.05). Human fear level did not affect reproductive performance or the growth of offspring (p > 0.05). The offspring of friendly gilts tended to have a more active response to the back test (p = 0.09), less freezing response in the open field test (p < 0.05), and received human contact more than piglets from fearful gilts (p < 0.05). The present study shows that gilt human fear level is linked to their stress levels, which can affect the personality of their piglets.

ABSTRACT Optimal feed efficiency (FE) in pigs is important for economic and environmental reasons. Previous research identified FE-associated bacterial taxa within the intestinal microbiota of growing pigs. This study investigated whether FE-associated bacteria and selected FE-associated physiological traits were consistent across geographic locations (Republic of Ireland [ROI] [two batches of pigs, ROI1 and ROI2], Northern Ireland [NI], and Austria [AT]), where differences in genetic, dietary, and management factors were minimized. Pigs (n = 369) were ranked, within litter, on divergence in residual feed intake (RFI), and 100 extremes were selected (50 with high RFI and 50 with low RFI) across geographic locations for intestinal microbiota analysis using 16S rRNA amplicon sequencing and examination of FE-associated physiological parameters. Microbial diversity varied by geographic location and intestinal sampling site but not by RFI rank, except in ROI2, where more-feed-efficient pigs had greater ileal and cecal diversity. Although none of the 188 RFI-associated taxonomic differences found were common to all locations/batches, Lentisphaerae, Ruminococcaceae, RF16, Mucispirillum, Methanobrevibacter, and two uncultured genera were more abundant within the fecal or cecal microbiota of low-RFI pigs in two geographic locations and/or in both ROI batches. These are major contributors to carbohydrate metabolism, which was reflected in functional predictions. Fecal volatile fatty acids and salivary cortisol were the only physiological parameters that differed between RFI ranks. Despite controlling genetics, diet specification, dietary phases, and management practices in each rearing environment, the rearing environment, encompassing maternal influence, herd health status, as well as other factors, appears to impact intestinal microbiota more than FE. IMPORTANCE Interest in the role of intestinal microbiota in determining FE in pigs has increased in recent years. However, it is not known if the same FE-associated bacteria are found across different rearing environments. In this study, geographic location and intestinal sampling site had a greater influence on the pig gut microbiome than FE. This presents challenges when aiming to identify consistent reliable microbial biomarkers for FE. Nonetheless, seven FE-associated microbial taxa were common across two geographic locations and/or two batches within one location, and these indicated a potentially “healthier” and metabolically more capable microbiota in more-feed-efficient pigs. These taxa could potentially be employed as biomarkers for FE, although bacterial consortia, rather than individual taxa, may be more likely to predict FE. They may also merit consideration for use as probiotics or could be targeted by dietary means as a strategy for improving FE in pigs in the future.

Fecal microbiota transplants (FMT) may be used to improve chicken’s feed efficiency (FE) via modulation of the intestinal microbiota and microbe-host signaling. This study investigated the effect of the administration of FMT from highly feed efficient donors early in life on the jejunal and cecal microbiota, visceral organ size, intestinal morphology, permeability, and expression of genes for nutrient transporters, barrier function and innate immune response in chickens of diverging residual feed intake (RFI; a metric for FE). Chicks (n = 110) were inoculated with the FMT or control transplant (CT) on 1, 6, and 9 days posthatch (dph), from which 56 chickens were selected on 30 dph as the extremes in RFI, resulting in 15 low and 13 high RFI chickens receiving the FMT and 14 low and 14 high RFI chickens receiving the CT. RFI rank and FMT only caused tendencies for alterations in the jejunal microbiota and only one unclassified Lachnospiraceae genus in cecal digesta was indicative of high RFI. By contrast, the FMT caused clear differences in the short-chain fatty acid (SCFA) profile in the crop and cecal microbiota composition compared to the CT, which indicated alterations in amylolytic, pullulanolytic and hemicellulolytic bacteria such as Lactobacillus, Dorea, and Ruminococcus. Moreover, the FMT caused alterations in intestinal development as indicated by the longer duodenum and shallower crypts in the ceca. From the observed RFI-associated variation, energy-saving mechanisms and moderation of the mucosal immune response were indicated by higher jejunal permeability, shorter villi in the ileum, and enhanced cecal expression of the anti-inflammatory cytokine IL10 in low RFI chickens. Relationships obtained from supervised multigroup data integration support that certain bacteria, including Ruminococcocaceae-, Lactobacillus-, and unclassified Clostridiales-phylotypes, and SCFA in jejunal and cecal digesta modulated expression levels of cytokines, tight-junction protein OCLN and nutrient transporters for glucose and SCFA uptake. In conclusion, results suggest that the intestine only played a moderate role for the RFI-associated variation of the present low and high RFI phenotypes, whereas modulating the early microbial colonization resulted in long-lasting changes in bacterial taxonomic and metabolite composition as well as in host intestinal development.

ABSTRACT Salmonella colonization and infection in production animals such as pigs are a cause for concern from a public health perspective. Variations in susceptibility to natural infection may be influenced by the intestinal microbiota. Using 16S rRNA compositional sequencing, we characterized the fecal microbiome of 15 weaned pigs naturally infected with Salmonella at 18, 33, and 45 days postweaning. Dissimilarities in microbiota composition were analyzed in relation to Salmonella infection status (infected, not infected), serological status, and shedding pattern (nonshedders, single-point shedders, intermittent-persistent shedders). Global microbiota composition was associated with the infection outcome based on serological analysis. Greater richness within the microbiota postweaning was linked to pigs being seronegative at the end of the study at 11 weeks of age. Members of the Clostridia, such as Blautia, Roseburia, and Anaerovibrio, were more abundant and part of the core microbiome in nonshedder pigs. Cellulolytic microbiota (Ruminococcus and Prevotella) were also more abundant in noninfected pigs during the weaning and growing stages. Microbial profiling also revealed that infected pigs had a higher abundance of Lactobacillus and Oscillospira, the latter also being part of the core microbiome of intermittent-persistent shedders. These findings suggest that a lack of microbiome maturation and greater proportions of microorganisms associated with suckling increase susceptibility to infection. In addition, the persistence of Salmonella shedding may be associated with an enrichment of pathobionts such as Anaerobiospirillum. Overall, these results suggest that there may be merit in manipulating certain taxa within the porcine intestinal microbial community to increase disease resistance against Salmonella in pigs. IMPORTANCE Salmonella is a global threat for public health, and pork is one of the main sources of human salmonellosis. However, the complex epidemiology of the infection limits current control strategies aimed at reducing the prevalence of this infection in pigs. The present study analyzes for the first time the impact of the gut microbiota in Salmonella infection in pigs and its shedding pattern in naturally infected growing pigs. Microbiome (16S rRNA amplicon) analysis reveals that maturation of the gut microbiome could be a key consideration with respect to limiting the infection and shedding of Salmonella in pigs. Indeed, seronegative animals had higher richness of the gut microbiota early after weaning, and uninfected pigs had higher abundance of strict anaerobes from the class Clostridia, results which demonstrate that a fast transition from the suckling microbiota to a postweaning microbiota could be crucial with respect to protecting the animals.

ABSTRACT Differences in chickens’ feed intake may be the underlying factor influencing feed-efficiency (FE)-associated variation in intestinal microbiota and physiology. In chickens eating the same amount of feed, quantitative feed restriction may create similar intestinal conditions and help clarify this cause-and-effect relationship. This study investigated the effect of ad libitum versus restrictive feeding (85% of ad libitum) on ileal and cecal microbiota, concentrations of short-chain fatty acids, visceral organ size, intestinal morphology, permeability, and expression of genes related to nutrient uptake, barrier function, and innate immune response in broiler chickens with divergent residual feed intake (RFI; metric for FE). On day 30 posthatch, 28 low-RFI (good FE) and 29 high-RFI (poor FE) chickens across both feeding-level groups (n = 112) were selected. Supervised multigroup data integration and relevance network analyses showed that especially Lactobacillus (negative) in ileal digesta, Turicibacter (positive) in cecal digesta, and Enterobacteriaceae (positive) in both intestinal segments depended on chicken’s feed intake, whereas the level of Anaerotruncus in cecal digesta was most discriminative for high RFI. Moreover, shallower crypts and fewer goblet cells in ceca indicated host-related energy-saving mechanisms with low RFI, whereas greater tissue resistance suggested a stronger jejunal barrier function in low-RFI chickens. Values corresponding to feed intake level × RFI interactions indicated larger pancreas and lower levels of ileal and cecal short-chain fatty acids in restrictively fed high-RFI chickens than in the other 3 groups, suggesting host physiological adaptations to support greater energy and nutrient needs of high-RFI chickens compensating for the restricted feeding. IMPORTANCE The impact of the FE-associated differences in feed intake on intestinal bacterial and host physiological parameters has so far not been clarified. Understanding the underlying principles is essential for the development of cost-effective strategies to improve FE in chicken production. Under conditions of quantitative feed restriction, low- and high-RFI chickens ate the same amount of feed. Therefore, this research helps in distinguishing intestinal bacterial taxa and functions that were highly reliant on feed intake from those that were associated with physiological adaptations to RFI-associated differences in host nutritional needs and intestinal nutrient availability. This work provides a background for further research to assess manipulation of the intestinal microbiota, host physiology, and FE in chickens by dietary intervention.

Liver is a metabolically complex organ that influences nutrient partitioning and potentially modulates the efficiency of converting energy acquired from macronutrients ingestion into a muscle and/or adipose tissue (referred to as feed efficiency, FE). The objective of this study was to sequence the hepatic tissue transcriptome of closely related but differently feed efficient pigs (n = 16) and identify relevant biological processes that underpin the differences in liver phenotype between FE groups. Liver weight did not significantly differ between the FE groups, however, blood parameters showed that total protein, glucose, cholesterol and percentage of lymphocytes were significantly greater in high-FE pigs. Ontology analysis revealed carbohydrate, lipid and protein metabolism to be significantly enriched with differentially expressed genes. In particular, high-FE pigs exhibited gene expression patterns suggesting improved absorption of carbohydrates and cholesterol as well as enhanced reverse cholesterol transport. Furthermore, the inferred decrease in bile acid synthesis in high-FE pigs may contribute to the observed greater levels of serum glucose, which can be then delivered to cells and utilized for growth and maintenance. Gene ontology analysis also suggested that livers of more efficient pigs may be characterized by higher protein turnover and increased epithelial cell differentiation, whereby an enhanced quantity of invariant natural killer T-cells and viability of natural killer cells could induce a quicker and more effective hepatic response to inflammatory stimuli. Our findings suggest that this prompt hepatic response to inflammation in high-FE group may contribute to the more efficient utilization of nutrients for growth in these animals.

There is a great interest to understand the impact of the gut microbiota on host's nutrient use and FE in chicken production. Both chicken's feed intake and gut bacterial microbiota differ between high and low-feed efficient chickens. To evaluate the impact of the feed intake level on the feed efficiency (FE)-associated variation in the chicken intestinal microbiota, differently feed efficient chickens need to eat the same amount of feed, which can be achieved by feeding chickens restrictively. Therefore, we investigated the effect of restrictive vs. ad libitum feeding on the fecal microbiome at 16 and 29 days posthatch (dph), FE and nutrient retention in chickens of low and high residual feed intake (RFI; metric for FE). Restrictively fed chickens were provided the same amount of feed which corresponded to 85% of the ad libitum fed group from 9 dph. FE was determined for the period between 9 and 30 dph and feces for nutrient retention were collected on 31 to 32 dph. From the 112 chickens (n = 56 fed ad libitum, and n = 56 fed restrictively), 14 low RFI and 15 high RFI ad libitum fed chickens, and 14 low RFI (n = 7 per sex) and 14 high RFI restrictively fed chickens were selected as the extremes in RFI and were retrospectively chosen for data analysis. Bray-Curtis dissimilarity matrices showed significant separation between time points, and feeding level groups at 29 dph for the fecal bacterial communities. Relevance networking indicated positive associations between Acinetobacter and feed intake at 16 dph, whereas at 29 dph Escherichia/Shigella and Turicibacter positively and Lactobacillus negatively correlated to chicken's feed intake. Enterobacteriaceae was indicative for low RFI at 16 dph, whereas Acinetobacter was linked to high RFI across time points. However, restrictive feeding-associated changes in the fecal microbiota were not similar in low and high RFI chickens, which may have been related to the higher nutrient retention and thus lower fecal nutrient availability in restrictively fed high RFI chickens. This may also explain the decreased RFI value in restrictively fed high RFI chickens indicating improved FE, with a stronger effect in females.

This review summarises the evidence for a link between the porcine intestinal microbiota and growth and feed efficiency (FE), and suggests microbiota-targeted strategies to improve productivity. However, there are challenges in identifying reliable microbial predictors of host phenotype; environmental factors impact the microbe–host interplay, sequential differences along the intestine result in segment-specific FE- and growth-associated taxa/functionality, and it is often difficult to distinguish cause and effect. However, bacterial taxa involved in nutrient processing and energy harvest, and those with anti-inflammatory effects, are consistently linked with improved productivity. In particular, evidence is emerging for an association of Treponema and methanogens such as Methanobrevibacter in the small and large intestines and Lactobacillus in the large intestine with a leaner phenotype and/or improved FE. Bacterial carbohydrate and/or lipid metabolism pathways are also generally enriched in the large intestine of leaner pigs and/or those with better growth/FE. Possible microbial signalling routes linked to superior growth and FE include increased intestinal propionate production and reduced inflammatory response. In summary, the bacterial taxa and/or metabolic pathways identified here could be used as biomarkers for FE/growth in pigs, the taxa exploited as probiotics or the taxa/functionality manipulated via dietary/breeding strategies in order to improve productivity in pigs.

This paper reviews the current knowledge on the nutritional requirements of entire male and immunocastrated pigs to obtain an efficient growth, low boar taint level, and good carcass and meat quality. We present the reasons for offering entire males ad libitum access to the diets in order to optimize their protein deposition potential. Boar taint is one of the major issues in the production of entire males; therefore, the impact of various skatole- and indole-reducing feed ingredients is discussed regarding their efficiency and the possible mechanism affecting skatole and indole production in the hindgut. Entire males have lean carcasses, so their intramuscular fat content can be lower than that of surgical castrates or females and the adipose tissue can be highly unsaturated. The possible nutritional strategies to counteract these effects are summarized. We conclude that immunocastrates can be fed similarly to entire males until the second vaccination. However, due to the metabolic changes occurring shortly after the second vaccination, the requirements for essential amino acids are markedly lower in immunocastrates than in entire males.

The composition of the intestinal microbiota plays an important role in the digestion and utilization of nutrients and for gut health. Low-fiber diets stimulate digestion and absorption processes, predominantly in the upper region of the gastrointestinal tract, thereby increasing the conversion of feed into body weight. As a consequence, the chemical composition of digesta after duodenal and jejunal absorption processes and passage has a limited complexity affecting colonization and molecular profiles of enterocytes in the hind gut. To decipher ileal and caecal microbial ecosystems and host transcriptional profiles that are beneficial for effective use of the remaining nutrients, pigs differing in feeding efficiency were studied. Biological functions that were consistently enriched at both the gene and microbiota levels comprise immunity-related processes, which ensure the integrity of the gastrointestinal tract. In addition, the differential abundance of certain genera, including Rothia, Subdoligranulu, Leeia and Cellulosilyticum, reflects the establishment of a microbial profile that supports the digestion of endogenously indigestible dietary components in highly feed-efficient pigs. Overall, the results indicate the potential to promote these beneficial functions and further improve feed efficiency through manipulation of dietary and probiotic strategies.

ABSTRACT Previous studies suggest a link between intestinal microbiota and porcine feed efficiency (FE). Therefore, we investigated whether fecal microbiota transplantation (FMT) in sows and/or neonatal offspring, using inocula derived from highly feed-efficient pigs, could improve offspring FE. Pregnant sows were assigned to control or FMT treatments and the subsequent offspring to control treatment, FMT once (at birth), or FMT four times (between birth and weaning). FMT altered sow fecal and colostrum microbiota compositions and resulted in lighter offspring body weight at 70 and 155 days of age when administered to sows and/or offspring. This was accompanied by FMT-associated changes within the offspring’s intestinal microbiota, mostly in the ileum. These included transiently higher fecal bacterial diversity and load and numerous compositional differences at the phylum and genus levels (e.g., Spirochaetes and Bacteroidetes at high relative abundances and mostly members of Clostridia, respectively), as well as differences in the abundances of predicted bacterial pathways. In addition, intestinal morphology was negatively impacted, duodenal gene expression altered, and serum protein and cholesterol concentrations reduced due to FMT in sows and/or offspring. Taken together, the results suggest poorer absorptive capacity and intestinal health, most likely explaining the reduced body weight. An additive effect of FMT in sows and offspring also occurred for some parameters. Although these findings have negative implications for the practical use of the FMT regime used here for improving FE in pigs, they nonetheless demonstrate the enormous impact of early-life intestinal microbiota on the host phenotype. IMPORTANCE Here, for the first time, we investigate FMT as a novel strategy to modulate the porcine intestinal microbiota in an attempt to improve FE in pigs. However, reprogramming the maternal and/or offspring microbiome by using fecal transplants derived from highly feed-efficient pigs did not recapitulate the highly efficient phenotype in the offspring and, in fact, had detrimental effects on lifetime growth. Although these findings may not be wholly attributable to microbiota transplantation, as antibiotic and purgative were also part of the regime in sows, similar effects were also seen in offspring, in which these interventions were not used. Nonetheless, additional work is needed to unravel the effects of each component of the FMT regime and to provide additional mechanistic insights. This may lead to the development of an FMT procedure with practical applications for the improvement of FE in pigs, which could in turn improve the profitability of pig production.

Among the zoonotic pathogens affecting pigs, Salmonella stands out due to the high number of human cases linked to pork consumption. In the last two decades many countries have put considerable effort into the control of the infection by surveillance and control strategies on farm. Despite this effort, many herds still have a high Salmonella prevalence and they require guidance to address this problem. The present study, using the serological surveillance data of finishing pigs from the Irish National pig Salmonella Control Programme, aimed to highlight factors associated with increased risk or that might mitigate Salmonella occurrence on farm. A questionnaire with 33 questions regarding herd characteristics, management, feeding, biosecurity, and health was completed for 61 individual herds. After the multivariate analysis by linear regression, nine variables were retained in the final model and linked to herd seroprevalence. Home produced-feed linked to the use of meal showed an eight points reduction in Salmonella prevalence compared to purchased feed (p = 0.042). Different biosecurity measures were associated to lower seroprevalence. Changing of footwear from outside to inside the farm decreased seroprevalence nearly 20 units (p = 0.014) and policies not permitting access to the farmyard to feed trucks (p = 0.048) or avoiding the presence of cats on the farm (p = 0.05) were estimated in 10 units less of seroprevalence. In contrast, the lack of perimeter fence increased the chance to have higher seroprevalence in five units (p = 0.05). Finally, intestinal diseases such as swine dysentery (p = 0.044) and E. coli diarrhea (p = 0.1) were estimated to increase Salmonella prevalence in ~20 and 10 units, respectively, demonstrating the importance of controlling other enteric pathogens in an on-farm Salmonella control programme. These results show the usefulness of surveillance data to improve on-farm control and confirm that Salmonella infection in pigs is multi-factorial and the approach to its control should be multifaceted.

Six antimicrobial-producing seaweed-derived Bacillus strains were evaluated in vitro as animal probiotics, in comparison to two Bacillus from an EU-authorized animal probiotic product. Antimicrobial activity was demonstrated on solid media against porcine Salmonella and E. coli. The marine isolates were most active against the latter, had better activity than the commercial probiotics and Bacillus pumilus WIT 588 also reduced E. coli counts in broth. All of the marine Bacillus tolerated physiological concentrations of bile, with some as tolerant as one of the probiotics. Spore counts for all isolates remained almost constant during incubation in simulated gastric and ileum juices. All of the marine Bacillus grew anaerobically and the spores of all except one isolate germinated under anaerobic conditions. All were sensitive to a panel of antibiotics and none harbored Bacillus enterotoxin genes but all, except B. pumilus WIT 588, showed some degree of β-hemolysis. However, trypan blue dye exclusion and xCELLigence assays demonstrated a lack of toxicity in comparison to two pathogens; in fact, the commercial probiotics appeared more cytotoxic than the majority of the marine Bacillus. Overall, some of the marine-derived Bacillus, in particular B. pumilus WIT 588, demonstrate potential for use as livestock probiotics.

Low birth weight piglets are at high risk of mortality, because of the rapid depletion of their energy reserves after birth. At 3 h postpartum, 405 piglets weighing n = 107 piglets), (2) commercial product (CP, 71 kJ/2 mL, n = 101 piglets), (3) water (W, 0 kJ/2 mL, n = 100 piglets) or (4) were sham-dosed (S, n = 97 piglets). Treatments were applied within litter (97 sows). Before treatment piglets were weighed, scored for vitality and blood glucose concentration (subset: CO = 45 piglets, CP = 38 piglets, W = 49 piglets and S = 44 piglets) and rectal temperature were measured. Rectal temperature was remeasured 1 h post-treatment (4 h postpartum). At 24 h post-treatment (27 h postpartum), vitality, weight and blood glucose were remeasured. Piglets were weighed on D5, D7, D10, D14, D21 and at weaning (27 ± 0.1 day old). Mortality rate and cause were recorded until 24h period post-treatment and until weaning. Data were analysed using Generalised Linear Mixed Models in SAS. There was no overall effect of treatment on any of the parameters measured. In conclusion, a single oral of fat-based energy supplement dose at birth did not improve growth, survival, rectal temperature or vitality of low birth weight piglets.

Restrictive feeding influences systemic metabolism of nutrients; however, this impact has not been evaluated in chickens of diverging feed efficiency. This study investigated the effect of ad libitum versus restrictive feeding (85% of ad libitum) on the serum metabolome and white blood cell composition in chickens of diverging residual feed intake (RFI; metric for feed efficiency). Blood samples were collected between days 33 and 37 post-hatch. While serum glucose was similar, serum uric acid and cholesterol were indicative of the nutritional status and chicken’s RFI, respectively. Feed restriction and RFI rank caused distinct serum metabolome profiles, whereby restrictive feeding also increased the blood lymphocyte proportion. Most importantly, 10 amino acids were associated with RFI rank in birds, whereas restrictive feeding affected almost all detected lysophosphatidylcholines, with 3 being higher and 6 being lower in restrictively compared to ad libitum fed chickens. As indicated by relevance networking, isoleucine, lysine, valine, histidine, and ornithine were the most discriminant for high RFI, whereas 3 biogenic amines (carnosine, putrescine, and spermidine) and 3 diacyl-glycerophospholipids (38:4, 38:5, and 40:5) positively correlated with feed intake and body weight gain, respectively. Only for taurine, feed intake mostly explained the RFI-associated variation, whereas for most metabolites, other host physiological factors played a greater role for the RFI-associated differences, and was potentially related to insulin-signaling, phospholipase A2, and arachidonic acid metabolism. Alterations in the hepatic synthesis of long-chain fatty acids and the need for precursors for gluconeogenesis due to varying energy demand may explain the marked differences in serum metabolite profiles in ad libitum and restrictively fed birds.

The objectives of this study were (1) to assess the bacteriocinogenic potential of bacteria derived mainly from seaweed, but also sand and seawater, (2) to identify at least some of the bacteriocins produced, if any and (3) to determine if they are unique to the marine environment and/or novel. Fifteen Bacillus licheniformis or pumilus isolates with antimicrobial activity against at least one of the indicator bacteria used were recovered. Some, at least, of the antimicrobials produced were bacteriocins, as they were proteinaceous and the producers displayed immunity. Screening with PCR primers for known Bacillus bacteriocins revealed that three seaweed-derived Bacillus licheniformis harbored the bli04127 gene which encodes one of the peptides of the two-peptide lantibiotic lichenicidin. Production of both lichenicidin peptides was then confirmed by mass spectrometry. This is the first definitive proof of bacteriocin production by seaweed-derived bacteria. The authors acknowledge that the bacteriocin produced has previously been discovered and is not unique to the marine environment. However, the other marine isolates likely produce novel bacteriocins, as none harboured genes for known Bacillus bacteriocins.

Background:Starch is a main source of glucose and energy in the human diet. The extent to which it is digested in the gastrointestinal tract plays a major role in variations in postprandial blood glucose levels. Interactions with other biopolymers, such as dairy proteins, during processing can influence both the duration and extent of this postprandial surge.Objective:To evaluate the effect of the addition of bovine α- or β-casein to waxy maize starch on changes in postprandial blood glucose, insulin, and incretin hormones [glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide 1 (GLP-1)] in 30 kg pigs used as an animal model for humans.Design:Gelatinised starch, Results:starch gelatinised with α-casein, and starch gelatinised with β-casein were orally administered to trained pigs (n = 8) at a level of 60 g of available carbohydrate. Pre- and postprandial glucose measurements were taken every 15 min for the first hour and every 30 min thereafter up to 180 min. Insulin, GIP, and GLP-1 levels were measured in plasma samples up to 90 min postprandial.Starch gelatinised with α-casein had a significantly (p < 0.05) lower peak viscosity on pasting and resulted in significantly lower glucose release at 15, 30, and 90 min postprandial compared to starch gelatinised with β-casein. During the first 45-min postprandial, the area under the glucose curve (AUC) for starch gelatinised with α-casein was significantly (p < 0.05) lower than that for starch gelatinised with β-casein. There was also a significant (p < 0.05) difference at T30 in GIP levels in response to the control compared to starch gelatinised with α- or β-casein. Significant (p < 0.05) increases in several free amino acid concentrations were observed on ingestion of either α- or β-casein gelatinised with starch at 30 and 90 min postprandial compared to starch alone. In addition, plasma levels of six individual amino acids were increased on ingestion of starch gelatinised with α-casein compared to ingestion of starch gelatinised with β-casein.Conclusion:The presence of casein fractions (α- or β-casein) in gelatinised waxy maize starch affects swelling characteristics, viscosity, and subsequent in vivo digestion as determined by glucose levels in blood postingestion.

The marine environment is an untapped source of bioactive compounds. Specifically, marine macroalgae (seaweeds) are rich in polysaccharides that could potentially be exploited as prebiotic functional ingredients for both human and animal health applications. Prebiotics are non-digestible, selectively fermented compounds that stimulate the growth and/or activity of beneficial gut microbiota which, in turn, confer health benefits on the host. This review will introduce the concept and potential applications of prebiotics, followed by an outline of the chemistry of seaweed polysaccharides. Their potential for use as prebiotics for both humans and animals will be highlighted by reviewing data from both in vitro and in vivo studies conducted to date.

The fetal and early postnatal environment can have a long-term influence on offspring growth. Using a pig model, we investigated the effects of maternal body condition (thin or fat) and maternal gestation feeding level (restricted, control or high) on maternal stress, milk composition, litter size, piglet birth weight and pre-weaning growth. A total of sixty-eight thin (backfat depth about 8 mm) and seventy-two fat (backfat depth about 12 mm) gilts were selected at about 22 weeks. This backfat difference was then accentuated nutritionally up to service at about 32 weeks. During gestation, individual gilts from within each group were randomly allocated to a gestation diet at the following feed allowances: 1·8 kg/d (restricted); 2·5 kg/d (control) and 3·5 kg/d (high) until day 90 of gestation. During gestation restricted gilts had higher levels of cortisol than high and control fed animals. Piglets born to fat gilts had higher average daily gain during the lactation period and higher weaning weights at day 28 than piglets born to thin gilts. Gilts on a high feed level had heavier piglets than those provided with restricted and control allocations. Fat gilts had less saturated fat in their milk at day 21 of lactation and higher unsaturated fat levels. No differences were found in the n-6:n-3 PUFA ratio in the milk between thin and fat gilts. In conclusion, maternal body condition influenced the daily weight gain of offspring up to weaning (day 28) and milk fat composition. Furthermore, maternal feed level during gestation alters maternal cortisol levels and milk fat composition.

Sample preservation and recovery of intact DNA from gut samples may affect the inferred gut microbiota composition in pigs. This study aimed to evaluate the effect of the freezing process and storage temperature prior to DNA extraction on DNA recovery and bacterial community composition in pig feces using quantitative PCR. Fresh fecal samples from six growing pigs were collected and five aliquots of each prepared: (1) total DNA extracted immediately; (2) stored at −20 °C; (3) snap frozen and stored at −20 °C; (4) stored at −80 °C; and (5) snap frozen and stored at −80 °C. Results showed that DNA yields from fresh fecal samples were, on average, 25 to 30 ng higher than those from the various stored samples. The DNA extracted from fresh samples had more gene copies of total bacteria and all targeted bacterial groups per gram feces compared to DNA extraction from frozen samples. Data presentation also modified the observed effect of freeze storage; as results for Lactobacillus group, Enterococcus spp., Streptococcus spp., Clostridium cluster IV, Bacteroides-Prevotella-Porphyromonas and Enterobacteriaceae showed the opposite effect when expressed as relative abundance, by being greater in freeze stored feces than in fresh feces. Snap freezing increased the relative proportion of Clostridium cluster IV by 24%. In conclusion, the freezing process affected DNA yield and bacterial abundances, whereas snap freezing and storage temperature had only little influence on abundances of bacterial populations in pig feces.