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The objective of this study was to determine the effect of bitter gourd (BG) leftovers (stems and leaves) as an alternative dietary ingredient on pig performance, carcass characteristics, serum parameters (urea, insulin, and leptin levels), and faecal consistency. Healthy Tempo × Great Yorkshire and Landrace pigs (N = 240; 120 gilts and 120 boars) weighing 25.8 kg (9–10 weeks of age) were randomly assigned to three treatments (eight pens per treatment; each pen with five gilts and five boars). The three treatments consisted of a non-supplemented commercial diet (control; CON) and a CON diet supplemented with 6.5 g/kg BG (BG1) or 13 g/kg BG (BG2). Pigs were fed the experimental diets until slaughter (120 kg body weight; BW). Feed intake was recorded daily and calculated for each experimental phase (i.e., days 0–36, days 36–66, days 66–98, and the overall experimental period). Average daily feed intake (ADFI), average daily gain (ADG), and feed conversion ratio (FCR) were calculated. The frequencies of visiting the feed station and of feeding were recorded daily. Faecal scores (FS) for consistency were measured per pen twice weekly. On the day of slaughter, two pigs per pen (one male and one female) were randomly selected for the measurement of muscle thickness and blood collection. At the slaughterhouse, carcass weight, dressing percentage, back fat thickness, muscle depth, and lean meat percentage were recorded. Data were analysed using ANOVA, with the pen as the experimental unit. Diets BG1 or BG2 did not affect the performance of the pigs, except for a significant decrease in the ADG of the pigs fed the BG2 diet in the feeding period of 50–80 kg. However, no differences in performance were observed in the overall experimental period. Faecal scores, carcass quality, and serum levels of urea, insulin, and leptin were also not affected by the diet. In summary, leftovers (stems and leaves) of BG can be successfully added to the diet of growing-finishing pigs without i

Around weaning, piglets are susceptible to infection by bacterial pathogens, leading to increased morbidity and mortality. We identified isolates of Rothia nasisuis in the upper respiratory tract of weaned healthy piglets that produce valinomycin in vitro and in vivo via a giant multimodule non-ribosomal peptide synthase (NRPS) enzyme complex. Valinomycin is an antiviral and antibiotic ionophore that shuttles potassium ions across membranes and is capable of inflammasome activation and apoptosis in LPS-primed macrophages. R. nasisuis inhibited growth of Streptococcus and Rothia species inhabiting the same niche. To investigate the potential for the valinomycin-producing Rothia nasisuis strain to colonize new-born piglets we performed a colonization study in newborn litters of piglets. Briefly, the newborn piglets of 3 sows farrowing on the same day were randomized between the three sows to avoid genetic bias in the experiment. The sows were housed in separate maternity pens and the piglets marked so they could be identified during the study. 9 of the 12 piglets nursed by sows A and B (further referred to as litters A and B) were orally administered approximately 10exp9 CFU of valinomycin-producing R. nasisuis, using a syringe on d2, d19 and d27 after birth. Three 3 piglets in litters A and B were not inoculated with R. nasisuis to see if they became colonized by horizontal transfer. As a control group all the piglets housed with the sow C (further referred to as litter C) were not inoculated with R. nasisuis.

Feeding strategies in early life have been shown to modulate piglet gut health, but effects on disease susceptibility have yet to be explained. We aimed to study effects of dietary-fibre-enriched diets fed to sows around farrowing (transition diet) and to suckling piglets (creep feed) on post-weaning gut health of piglets challenged with enterotoxigenic Escherichia coli (ETEC).

The aim of the present study was to assess the absence of a non-starch polysaccharide (NSP) enzyme in a broiler diet containing a low level (10%) of rye inclusion. Two experimental groups with 40 Ross broilers each, were fed a diet containing 10% rye. One group was supplemented with a NSP enzyme, and the other was not supplemented with the enzyme to increase intestinal viscosity. The birds were fed the respective diets for 14 or 28 days. Intestinal sections were submitted to morphological, morphometric and mRNA-level gene expression analyses. To assess gut leakage, 150 min before euthanasia, broilers had no access to feed and received an oral gavage with fluorescein isothiocyanate-labelled dextran (FITC-d). Serum levels of FITC-d, D-lactate, tight-junction-associated protein 1 (TJAP1), citrulline and ovotransferrin were determined. A significant increase in FITC-d levels was observed in the 14-day-old birds fed the non-supplemented rye diet, and no other serum markers were affected. These birds presented a decreased villus height/crypt depth (VH:CD) ratio and an increased degree of damage in the jejunum. The ileum VH:CD increased, and the goblet cell number decreased in 28-day-old birds fed the non-supplemented rye diet. When broilers were fed the non-supplemented rye diet, the mRNA expression of the tight-junction zona occludens 1 (ZO1) was significantly decreased in the jejunum of 14-day-old broilers, whereas a significant decrease in jejunum mRNA expression of ZO2 and mucin-2 (MUC2) was observed in the jejunum of 28-day-old broilers. In contrast, a significant increase in the mRNA expression of ZO2 was observed in the ileum from 28-day-old broilers fed the non-supplemented rye diet. In conclusion, a 10% rye diet causes intestinal stress in young broiler chickens when the feed is not supplemented with a NSP enzyme. This study may be applied as experimental model of mild gut leakage of broiler chickens.

Little is known about the development of the tonsillar microbiota and the factors determining the establishment and proliferation of disease-associated bacteria. In this study we sampled the tonsillar microbiota of 63 piglets from 21 different litters after birth and at week 1, 3, and 5 of life. The piglets were free from disease and antimicrobial treatment throughout the study period. 16S rRNA gene V3-V4 region Illumina NovaSeq sequencing produced a minimum of 42537 reads per sample after processing with DADA2. The dataset includes 252 piglet microbiota samples and 12 samples collected from unrelated sows at the same farm. Analysis revealed that a diverse tonsillar microbiota is established shortly after birth, and that gradual change takes place during the first 5 weeks of life without weaning having a large impact. We found a strong litter effect, with siblings sharing a more similar microbiota compared to non-sibling piglets. Co-housing in rooms, within which litters were housed in separate pens, also had a large impact on microbiota composition. Sow parity and pre-partum Streptococcus suis bacterin vaccination had weaker but significant associations with microbiota composition, with piglets of vaccinated sows having a lower S. suis abundance 1 week after birth. This dataset consists of 16S rRNA gene V3-V4 amplicon sequencing of tonsillar swabs of piglets. The piglets were sampled shortly after birth, at week 1, week 3, and (after being weaned at week 4), week 5. No antimicrobial treatment was applied, and all piglets were healthy; piglets that died during the experiment were not included for sequencing.

The advent of next-generation sequencing technologies allowed relative quantification of microbiome communities and their spatial and temporal variation. In recent years, supervised learning (i.e., prediction of a phenotype of interest) from taxonomic abundances has become increasingly common in the microbiome field. However, a gap exists between supervised and classical unsupervised analyses, based on computing ecological dissimilarities for visualization or clustering. Despite this, both approaches face common challenges, like the compositional nature of next-generation sequencing data or the integration of the spatial and temporal dimensions. Here we propose a kernel framework to place on a common ground the unsupervised and supervised microbiome analyses, including the retrieval of microbial signatures (taxa importances). We define two compositional kernels (Aitchison-RBF and compositional linear) and discuss how to transform non-compositional beta-dissimilarity measures into kernels. Spatial data is integrated with multiple kernel learning, while longitudinal data is evaluated by specific kernels. We illustrate our framework through a single point soil dataset, a human dataset with a spatial component, and a previously unpublished longitudinal dataset concerning pig production. The proposed framework and the case studies are freely available in the kernInt package at https://github.com/elies-ramon/kernInt.

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.