Effect of dietary fiber content on nutrient digestibility and fecal microbiota composition in growing-finishing pigs

Estimating the influence of dietary composition and management on nutrient intake and excretion and methane emission in different pig categories

The study aimed to estimate the effect of diet composition, pig production stage, in-housing conditions, and manure management on methane (CH4) emissions from enteric fermentation, manure stored in the barn, and the outdoor storage tank. For each pig category, an estimation for emissions was made for a standard Danish pig diet based on wheat, barley, and soybean meal. Within each category of pigs, emissions were also estimated for diets with different levels and types of dietary fiber from sugar beet pulp, wheat bran, oats, wheat, or soy hulls, which were included as a partial substitution for wheat or barley. In all diets within four pig categories, feed intake, excreted dry matter, feces mass, and urine volume (g/d per animal) increased in sugar beet pulp, wheat bran, oat, or soy hull diets compared to the average Danish diet. In grower-finisher pigs, the sum of CH4 emissions from enteric fermentation, manure stored in the barn, and the outdoor storage tank were 9.8, 10.2, 11.0, 11.0, and 11.2 (kg/year/animal place) for wheat diet, average Danish diet, oat diet, wheat bran diet, and sugar beet pulp diet, respectively, while in gestating sows, were 16.9, 17.5, 18.4, 19.6, 19.7, and 23.2 (kg/year/animal place) in wheat diet, average Danish diet, oat diet, sugar beet pulp diet, wheat bran diet, and soy hull diet, respectively. Contribution of CH4 emissions from manure stored in the barn plus outdoor storage tank for the average Danish diet accounted for 95, 90, 83, and 84% of total CH4 emissions in weaned pigs, grower-finisher pigs, lactating sows, and gestating sows, respectively. In conclusion, feed composition has a considerable impact on CH4 emissions. Enteric CH4 and CH4 emissions from manure stored in the barn and in the outdoor storage tank were increased by elevated concentration of residual fiber in all four pig categories except for enteric CH4 in weaned pigs.

Intrauterine growth restriction, defined by an elevated brain-to-liver weight ratio, affects faecal microbiota composition and, to a lesser extent, plasma metabolome profile at different ages in pigs

BACKGROUND

Intrauterine growth restriction (IUGR) affects up to 30% of piglets in a litter. Piglets exposed to IUGR prioritize brain development during gestation, resulting in a higher brain-to-liver weight ratio (BrW/LW) at birth. IUGR is associated with increased mortality, compromised metabolism, and gut health. However, the dynamic metabolic and microbial shifts in IUGR-affected pigs remain poorly understood. This study aimed to investigate the longitudinal effects of IUGR, defined by a high BrW/LW, on the composition of faecal microbiota and plasma metabolome in pigs from birth to slaughter. One day (± 1) after birth, computed tomography was performed on each piglet to assess their brain and liver weights. The pigs with the highest (IUGR = 12) and the lowest (NORM = 12) BrW/LW were selected to collect faeces and blood during lactation (day 16 ± 0.6, T1) and at the end of the starter period (day 63 ± 8.6, T2) and faeces at the beginning (day 119 ± 11.4, T3) and end of the finisher period (day 162 ± 14.3, T4).

RESULTS

Faecal microbial Alpha diversity remained unaffected by IUGR across all time points. However, the Beta diversity was influenced by IUGR at T1 (P = 0.002), T2 (P = 0.08), and T3 (P = 0.03). Specifically, IUGR pigs displayed higher abundances of Clostridium sensu stricto 1 (Padj = 0.03) and Romboutsia (Padj = 0.05) at T1, Prevotellaceae NK3B31 group (Padj = 0.02), Rikenellaceae RC9 gut group (Padj = 0.03), and Alloprevotella (Padj = 0.03) at T2, and p-2534-18B5 gut group (Padj = 0.03) at T3. Conversely, the NORM group exhibited higher abundances of Ruminococcus (Padj = 0.01) at T1, HT002 (Padj = 0.05) at T2, and Prevotella_9 (Padj < 0.001) at T3. None of the plasma metabolites showed significant differences at T1 between the IUGR and NORM pigs. However, at T2, asparagine was lower in the IUGR compared to the NORM group (P < 0.05).

CONCLUSIONS

These findings show that growth restriction in the uterus has a significant impact on the faecal microbiota composition in pigs, from birth to the beginning of the finisher period, but minimally affects the plasma metabolome profile.

Effects of dietary supplementation of myristic acid on jejunal mucosa-associated microbiota, mucosal immunity, and growth performance of nursery pigs

The objective of this study was to investigate the effects of myristic acid on jejunal mucosal microbiota, mucosal immunity, and growth performance of nursery pigs. Thirty-six pigs (6.6 ± 0.4 kg of body weight) were assigned to three treatments (n = 12) for 35 d in three phases: (NC) basal diet; (PC) NC + bacitracin; and (MA) NC + myristic acid compound. Pigs were euthanized to collect jejunal mucosa, jejunal tissues, and ileal digesta. The PC increased (p < 0.05) the relative abundance (RA) of Lactobacillus spp., and Bifidobacterium boum than the NC group. The MA increased (p < 0.05) RA of Bifidobacterium dentium and Megasphaera spp. than the NC group. The PC tended to decrease IL-8 (p = 0.053) and protein carbonyl (p = 0.075) whereas IgG (p = 0.051) and IL-8 (p = 0.090) in jejunal mucosa were decreased by the MA. The PC increased (p < 0.05) the villus height to crypt depth ratio than the NC group. Both bacitracin and myristic acid improved the intestinal health and growth performance of nursery pigs. Effects of bacitracin were rather immediate whereas the effects of myristic acid were obtained after a 3-week feeding.

Seasonal variations in composition and function of gut microbiota in grazing yaks: Implications for adaptation to dietary shift on the Qinghai-Tibet plateau

Gut microbiome of animals is affected by external environmental factors and can assist them in adapting to changing environments effectively. Consequently, elucidating the gut microbes of animals under different environmental conditions can provide a comprehensive understanding of the mechanisms of their adaptations to environmental change, with a particular focus on animals in extreme environments. In this study, we compared the structural and functional differences of the gut microbiome of grazing yaks between the summer and winter seasons through metagenomic sequencing and bioinformatics analysis. The results indicated that the composition and function of microbes changed significantly. The study demonstrated an increase in the relative abundance of Actinobacteria and a higher ratio of Firmicutes to Bacteroidetes (F/B) in winter, this process facilitated the adaptation of yaks to the consumption of low-nutrient forages in the winter. Furthermore, the network structure exhibited greater complexity in the winter. Forage nutrition exhibited a significant seasonal variation, with a notable impact on the gut microbiota. The metagenomic analysis revealed an increase in the abundance of enzymes related to amino acid metabolism, axillary activity, and mucin degradation in the winter. In conclusion, this study demonstrated that the gut microbiome of grazing yaks exhibits several adaptive characteristics that facilitate better nutrient accessibility and acid the host in acclimating to the harsh winter conditions. Furthermore, our study offers novel insights into the mechanisms of highland animal adaptation to external environments from the perspective of the gut microbiome.

Combination of β-mannanase plus multi-carbohydrase complex in simple or complex post-weaned pig diets on nutrient metabolism and gut health

This study was conducted to evaluate whether adding β-mannanase alone or in combination with a multi-carbohydrase complex to simple and complex diets could improve diet digestibility, nutrient and energy metabolism, and gut health in weaned pigs. Thirty pigs (7.9 kg ± 0.851 kg) weaned at 28 days were randomly split into a 2 × 3 factorial arrangement, considering a simple (corn and soybean meal-based diet) or complex diet (13% point reduction in inclusion of soybean meal, 5% of whey power, and 2.5% of spray-dried plasma compared to the simple diet) and diet without any addition (control) or the addition of β-mannanase (BM; 0.300 g/kg of the diet) or β-mannanase plus a multi-carbohydrase complex blend such as xylanase, β-glucanase, and arabinofuranosidases (BM + MCC; 0.300 + 0.050 g/kg of the diet) for 17 days post-weaned. Total fecal and urine samples were collected on days 11-17. Fecal samples were collected from all pigs to identify fecal biomarkers using commercial ELISA tests. Blood samples were collected from all pigs at the end of the experimental period to assess serum concentrations of acute-phase proteins. All pigs were euthanized on day 18 for intestinal tissue collection. The simple diet had greater (p < 0.05) protein digestibility and metabolizability coefficients than the complex diet. Greater (p < 0.05) energy digestibility and energy metabolizability coefficients were observed in the BM and BM+ MCC compared to the control diet. On average, BM improved by 64 kcal/kg and BM + MCC improved by 100 kcal/kg of metabolizable energy. Furthermore, the addition of BM and BM + MCC to the diets led to lower fecal moisture and fecal output. Moreover, the BM and BM + MCC diets also reduced fecal calprotectin concentrations by 29 and 46%, respectively, compared to control pigs (p < 0.001). We conclude that simple diets are a suitable alternative to complex diets, without compromising the nutrient digestibility and gut health of post-weaned pigs. The addition of exogenous enzymes improves nutrient and energy utilization, as well as the absorption area, and decreases calprotectin concentrations.

Impact of including two types of destoned olive cakes in pigs' diets on fecal bacterial composition and study of the relationship between fecal microbiota, feed efficiency, gut fermentation, and gaseous emissions

The microbial population in the pig's gastrointestinal tract can be influenced by incorporating fibrous by-products into the diets. This study investigated the impact of including two types of dried olive cake (OC) in pigs' diets on fecal bacterial composition. The correlation between fecal microbiota and growth performance, nutrient digestibility, gut fermentation pattern and slurry gas emissions was also evaluated. Thirty male Pietrain x (Landrace x Large white) pigs (47.9 ± 4.21 kg) were assigned to three groups: a control group (C), a group fed a diet with 20% partially defatted OC (20PDOC), and a group fed a diet with 20% cyclone OC (20COC) for 21 days. Fecal samples collected before and after providing the experimental diets were analyzed for the V3-V4 region of the 16S rRNA gene. Pigs were weighed, and feed intake was recorded throughout the study. Potential ammonia and methane emissions from slurry were measured. No significant differences in alpha diversity indexes were found. The taxonomic analysis revealed that Firmicutes and Bacteroidota phyla were dominant at the phylum level across all groups. Differential abundance analysis using ALDEx showed significant differences among groups for various bacteria at the phylum, genus, and species levels at the end of the experiment. Pigs from 20PDOC and 20COC groups exhibited increased abundances of health-promoting bacteria, such as Plactomycetota at the phylum level and Allisonella and an unidentified genus from the Eggerthellaceae family at the genus level. These changes influenced short-chain fatty acids' (SCFA) concentration in slurries, leading to greater acetic, butyric, caproic and heptanoic acids in OC-fed groups, especially 20COC pigs. A volatility analysis revealed significant positive correlations (p < 0.05) between Uncultured_Bacteroidales and Unculured_Selenomonadaceae and energy digestibility. Monoglobus and Desulfovibrio showed a positive significant (p < 0.05) correlation with total SCFA, indicating a high impact on gut fermentation. However, growth performance parameters and potential gas emission displayed no significant correlations with a specific bacterial genus. In conclusion, our results suggest that OC inclusion into pig diets could positively modulate and contribute to the gut microbiota's favorable composition and functionality. Also, nutrient digestibility and gut fermentation patterns can be associated with specific microbial populations.

Dietary crude protein time-dependently modulates the bacterial community and metabolites and changes dietary nutrient efficiency in growing pigs

The reduced nutrient digestibility of low-protein (LP) diets has been shown to be caused by the weakened fermentative capacity of the post-gut flora. The dynamic regulation of dietary protein contents on post-gut microbial population and fermentative metabolism is unclear. Twelve growing barrows (19.9 ± 0.8 kg) fitted with a T-cannula at the blind end of the cecum were randomly administered a high-protein (HP, 21.5% crude protein [CP]) diet or an LP (15.5% CP) diet for 28 d. The cecal content and feces were collected at d 1, 14, and 28 of the experiment for microflora structures and metabolite concentrations analysis. The nutrient digestibility coefficient and plasma biochemical parameters were also determined. Compared with the HP treatment, the LP treatment showed decreased plasma urea nitrogen concentration and apparent total tract digestibility of dry matter, gross energy, and CP (P < 0.01). In addition, urinary nitrogen losses, total nitrogen losses, and daily nitrogen retention in the LP treatment were lower than those in the HP treatment (P < 0.01), and the nitrogen retention-to-nitrogen intake ratio in the LP treatment was increased (P < 0.01). The HP group showed increased cecal total short-chain fatty acids (SCFA) concentration and fecal propionate, butyrate, and total SCFA concentrations (P < 0.05) on d 14 and 28, which may be mainly related to the elevated abundance of SCFA-producing bacteria, such as Ruminococcus, Lactobacillus, and Prevotella (P < 0.05). Probiotics, such as Bifidobacterium, Bacteroidales S24-7, and Rikenella, enriched in the LP treatment possibly contributed to reduced plasma endotoxin content. The differences in the abundances of almost all the above-mentioned flora appeared on d 28 but not d 14. Likewise, differences in the Simpson and Shannon indices and clustering patterns of the microbiota between treatments were also only observed on d 28. To sum up, in a time-dependent manner, the LP diet increased probiotics with gut-improving functions and decreased SCFA-producing bacteria, which may cause enhanced intestine health and reduced nutrient digestibility.

Interrelation between gut microbiota, SCFA, and fatty acid composition in pigs

The gut microbiota is a key player in the host metabolism. Some bacteria are able to ferment non-digestible compounds and produce short-chain fatty acids that the host can later transform and accumulate in tissue. In this study, we aimed to better understand the relationships between the microorganisms and the short-chain fatty acid composition of the rectal content, including the possible linkage with the fatty acid composition in backfat and muscle of the pig. We studied a Duroc × Iberian crossbred population, and we found significant correlations between different bacterial and archaeal genera and the fatty acid profile. The abundance of n-butyric acid in the rectal content was positively associated with Prevotella spp. and negatively associated with Akkermansia spp., while conversely, the abundance of acetic acid was negatively and positively associated with the levels of Prevotella spp. and Akkermansia spp., respectively. The most abundant genus, Rikenellaceae RC9 gut group, had a positive correlation with palmitic acid in muscle and negative correlations with stearic acid in backfat and oleic acid in muscle. These results suggest the possible role of Prevotella spp. and Akkermansia spp. as biomarkers for acetic and n-butyric acids, and the relationship of Rikenellaceae RC9 gut group with the lipid metabolism, building up the potential, although indirect, role of the microbiota in the modification of the backfat and muscle fatty acid composition of the host.IMPORTANCEThe vital role of the gut microbiota on its host metabolism makes it essential to know how its modulation is mirrored on the fatty acid composition of the host. Our findings suggest Prevotella spp. and Akkermansia spp. as potential biomarkers for the levels of beneficial short-chain fatty acids and the possible influence of Rikenellaceae RC9 gut group in the backfat and muscle fatty acid composition of the pig.

The potential of microbiota information to better predict efficiency traits in growing pigs fed a conventional and a high-fiber diet

BACKGROUND

Improving pigs' ability to digest diets with an increased dietary fiber content is a lever to improve feed efficiency and limit feed costs in pig production. The aim of this study was to determine whether information on the gut microbiota and host genetics can contribute to predict digestive efficiency (DE, i.e. digestibility coefficients of energy, organic matter, and nitrogen), feed efficiency (FE, i.e. feed conversion ratio and residual feed intake), average daily gain, and daily feed intake phenotypes. Data were available for 1082 pigs fed a conventional or high-fiber diet. Fecal samples were collected at 16 weeks, and DE was estimated using near‑infrared spectrometry. A cross-validation approach was used to predict traits within the same diet, for the opposite diet, and for a combination of both diets, by implementing three models, i.e. with only genomic (Gen), only microbiota (Micro), and both genomic and microbiota information (Micro+Gen). The predictive ability with and without sharing common sires and breeding environment was also evaluated. Prediction accuracy of the phenotypes was calculated as the correlation between model prediction and phenotype adjusted for fixed effects.

RESULTS

Prediction accuracies of the three models were low to moderate (< 0.47) for growth and FE traits and not significantly different between models. In contrast, for DE traits, prediction accuracies of model Gen were low (< 0.30) and those of models Micro and Micro+Gen were moderate to high (> 0.52). Prediction accuracies were not affected by the stratification of diets in the reference and validation sets and were in the same order of magnitude within the same diet, for the opposite diet, and for the combination of both diets. Prediction accuracies of the three models were significantly higher when pigs in the reference and validation populations shared common sires and breeding environment than when they did not (P < 0.001).

CONCLUSIONS

The microbiota is a relevant source of information to predict DE regardless of the diet, but not to predict growth and FE traits for which prediction accuracies were similar to those obtained with genomic information only. Further analyses on larger datasets and more diverse diets should be carried out to complement and consolidate these results.

Impact of an oligosaccharide-based polymer on the metabolic profiles and microbial ecology of weanling pigs experimentally infected with a pathogenic E. coli

BACKGROUND

Our previous study has reported that supplementation of oligosaccharide-based polymer enhances gut health and disease resistance of pigs infected with enterotoxigenic E. coli (ETEC) F18 in a manner similar to carbadox. The objective of this study was to investigate the impacts of oligosaccharide-based polymer or antibiotic on the host metabolic profiles and colon microbiota of weaned pigs experimentally infected with ETEC F18.

RESULTS

Multivariate analysis highlighted the differences in the metabolic profiles of serum and colon digesta which were predominantly found between pigs supplemented with oligosaccharide-based polymer and antibiotic. The relative abundance of metabolic markers of immune responses and nutrient metabolisms, such as amino acids and carbohydrates, were significantly differentiated between the oligosaccharide-based polymer and antibiotic groups (q < 0.2 and fold change > 2.0). In addition, pigs in antibiotic had a reduced (P < 0.05) relative abundance of Lachnospiraceae and Lactobacillaceae, whereas had greater (P < 0.05) Clostridiaceae and Streptococcaceae in the colon digesta on d 11 post-inoculation (PI) compared with d 5 PI.

CONCLUSIONS

The impact of oligosaccharide-based polymer on the metabolic and microbial profiles of pigs is not fully understood, and further exploration is needed. However, current research suggest that various mechanisms are involved in the enhanced disease resistance and performance in ETEC-challenged pigs by supplementing this polymer.

Effect of providing citrus pulp-integrated diet on fecal microbiota and serum and fecal metabolome shifts in crossbred pigs

The study aimed to assess the impact of dehydrated citrus pulp (DCP) on growth performance, fecal characteristics, fecal bacterial composition (based on 16S rRNA analysis), and fecal and serum metabolomic profiles in crossbred pigs. 80 finishing pigs Duroc × (Landrace × Large White) were fed either a control diet (C) or a diet with 240 g/kg DCP (T) for six weeks. Including DCP in diets tended to decrease feed intake, increased (p < 0.05) the concentrations of acetic and heptanoic acids and decreased (p < 0.05) fecal butyric and branched-chain fatty acid concentrations in feces. Animals fed DCP exhibited a lower abundance of the genera Clostridium and Romboutsia, while Lachnospira significantly increased. Orthogonal partial least squares discriminant analysis plotted a clear separation of fecal and serum metabolites between groups. The main discriminant fecal metabolites were associated with bacterial protein fermentation and were downregulated in T-fed pigs. In serum, DCP supplementation upregulated metabolites related to protein and fatty acids metabolism. In conclusion, the addition of DCP as an environmentally friendly source of nutrients in pig diets, resulted in modifications of fecal bacterial composition, fermentation patterns, and overall pig metabolism, suggesting improvements in protein metabolism and gut health.

Effect of Particle Size of Wheat and Barley Grain on the Digestibility and Fermentation of Carbohydrates in the Small and Large Intestines of Growing Pigs

The objective of this investigation was to study the effects of different cereal types, barley and wheat, with different particle sizes (PS) on the recovery of ileal digesta and fecal excretion, digestion of nutrients and fiber components, mean transit time (MTT), and short-chain fatty acid content and composition in growing pigs studied in two experiments. Five barrows with ileal cannulas (initial BW 35.9 ± 1.5 kg) in Experiment 1 and thirty-two castrated pigs (30.8 ± 1.3 kg) in Experiment 2 were fed four different diets: barley fine, barley coarse, wheat fine and wheat coarse diets. The cereal type and PS did not influence the relative weight of the small and large intestines and pH of digesta, whereas MTT in the large intestine of pigs fed the coarse barley diet was lower compared to pigs fed other diets (p < 0.05). Pigs fed the coarse barley diet had lower apparent ileal digestibility (AID) and apparent total tract digestibility (ATTD) of nutrients and fiber (p < 0.05), whereas pigs fed the fine barley diet had similar AID and ATTD to pigs fed wheat fine and coarse diets (p < 0.05). In conclusion, the barley diet was more influenced by PS in comparison to wheat, thereby inducing lower AID and ATTD of nutrient.

Characterization of the fecal microbiota of Pampa Rocha pigs, a genetic resource endemic to eastern Uruguay

Pampa Rocha (PR) is a breed of pig that emerged in eastern Uruguay during the 18th century. They represent an important resource for non-intensive production using purebred or crossbred animals. However, productive activities have been oriented towards intensive production using commercial breeds, abandoning, except by some academic and educational institutions, the promotion of this creole breed. Thus, a population of few animals is still maintained, which could be in danger of disappearing. This work focuses on the fecal microbiota of these animals, which is related to the animal genetic background but also to their grazing capacity and resistance to weather. The structure and diversity of bacterial communities in the intestines of four PR adult females and of other breeds, including crosses, reared under non-grazing conditions, were analyzed and compared. Results obtained indicate that PR fecal microbiota is clearly different from those of other animals analyzed. Some sequences, corresponding to particular groups apparently related to the consumption of fiber, were strongly associated with PR pigs.

Dietary micro-fibrillated cellulose improves growth, reduces diarrhea, modulates gut microbiota, and increases butyrate production in post-weaning piglets

Dietary fiber (DF) supplementation is one of the strategies to prevent on-farm infections; it has the capability to improve gut health and piglet performance. Among the beneficial DFs, micro-fibrillated cellulose (MFC) is a new-generation plant-derived innovative feed ingredient; MFC, originating from sugar-beet pulp, has a hyper-branched structure with the ability to form shear-thinning hydrogel and has a high water-binding capacity. We aimed to determine the effects of MFC supplementation on piglets' performance before and after weaning. We included 45 sows and their piglets in this trial and monitored the results until the piglets were 7 weeks old. Piglets supplemented with MFC had higher body weight and average daily growth (ADG) than did control piglets, both pre- and post-weaning. In addition, MFC supplementation in post-weaning piglets improved butyrate content, and reduced diarrhea incidence. These phenomena, perhaps due to the MFC supplementation at different stages until age 7 weeks. In addition, after weaning, MFC supplementation stimulated the growth of butyrate-producing bacteria such as Ruminococcus.2, Ruminococcaceae.UCG.014, Intestinibacter, Roseburia, and Oribacterium genera, as well as reduced the pathogenic bacteria, such as Campylobacter, and Escherichia. Evidently, supplementation of MFC in feed to young piglets can improve growth performance and butyric acid content and reduce post-weaning diarrhea.

Impacts of dietary fiber level on growth performance, apparent digestibility, intestinal development, and colonic microbiota and metabolome of pigs

This study aimed to investigate the roughage tolerance of different breeds of pigs. Mashen (MS; n = 80) and Duroc × Landrace × Yorkshire (DLY; n = 80) pigs with an initial body weight of 20 ± 0.5 kg were randomly allotted to four diet treatments (n = 20 of each breed) with different fiber levels. The dietary fiber levels increased by adding 0% to 28% soybean hull to replace corn and soybean meal partially. According to the neutral detergent fiber (NDF) level, all treatments were MS_9N (9% NDF), MS_13.5N (13.5% NDF), MS_18N (18% NDF), MS_22.5N (22.5% NDF), DLY_9N (9% NDF), DLY_13.5N (13.5% NDF), DLY_18N (18% NDF), and DLY_22.5N (22.5% NDF). The growth performance, nutrient digestibility, intestinal morphology, and colonic short-chain fatty acids of pigs were measured. The colonic microbiota and metabolome were analyzed using 16S rDNA gene sequencing and UHPLC-MS/MS. The average daily gain and daily feed intake of MS_18N and DLY_13.5N were increased compared with MS_9N and DLY_9N, respectively (P < 0.05). The digestibility of NDF and acid detergent fiber of MS_18N were greater than that of MS_9N (P < 0.05). The villus height/crypt depth (V/C) of the duodenum, jejunum, and ileum of MS_18N and MS_22.5N increased compared with MS_9N (P < 0.05), and the V/C of duodenum and ileum of DLY_22.5N decreased compared with DLY_9N (P < 0.05). The colonic acetic acid and butyric acid concentrations of MS_18N were greater than those of MS_9N and MS_13.5N (P < 0.05). The concentrations of acetic acid and butyric acid of DLY_13.5N increased compared with DLY_9N (P < 0.05). Prevotellaceae_NK3B31_group in MS_18N and Methanobrevibacter in MS_22.5N increased compared with other groups (P < 0.05). Increasing the NDF level in diets changed the lipid and amino acid metabolism pathways. In conclusion, appropriate fiber levels can promote pigs' growth performance and intestinal development. The optimum fiber level of the MS pig was 18% NDF, while that of the DLY pig was 13.5%. This result indicates that MS pigs had strong fiber fermentation ability due to the higher abundance of the colonic microbiota that could fully ferment fiber and provide extra energy to MS pigs.

An insight into the commercial piglet's microbial gut colonization: from birth towards weaning

BACKGROUND

The establishment of the gut microbiota can be influenced by several perinatal factors, including, most importantly, the maternal microbiota. Moreover, early-life environmental variation affects gut microbial colonization and the intestinal health of offspring throughout life. The present study aimed to explore the development of piglet gut microbiota from birth to weaning in the commercial practice and also to assess how different farm environments could condition this process. Although it is possible to find in the literature other studies with similar objectives this work probably represents one of the few studies that make a systematic evaluation of such differential factors under a real scenario. To achieve this objective, we performed two trials. In a first Trial, we selected 2 farms in which we performed an intensive sampling (5 samples /animal) to characterize the gut colonization pattern during the first days of life and to identify the time window with the greatest impact. Both farms differed in their health status and the use of antimicrobials in the piglets. In a second Trial, we selected 4 additional farms with variable rearing conditions and a distinctive use of antimicrobials in the sows with a simplified sampling pattern (2 samples/animal). Faecal samples were obtained with swabs and DNA was extracted by using the PSP® Spin Stool DNA Kit and sequencing of the 16S rRNA gene (V3-V4 region) performed by Illumina MiSeq Platform.

RESULTS

The present study contributes to a better understanding of microbiome development during the transition from birth to weaning in commercial conditions. Alpha diversity was strongly affected by age, with an increased richness of species through time. Beta diversity decreased after weaning, suggesting a convergent evolvement among individuals. We pinpointed the early intestinal colonizers belonging to Bacteroides, Escherichia-Shigella, Clostridium sensu stricto 1, and Fusobacterium genera. During lactation(d7-d21 of life), the higher relative abundances of Bacteroides and Lactobacillus genera were correlated with a milk-oriented microbiome. As the piglets aged and after weaning (d36 of life), increasing abundances of genera such as Prevotella, Butyricimonas, Christensenellaceae R-7 group, Dorea, Phascolarctobacterium, Rikenellaceae RC9 gut group, Subdoligranulum, and Ruminococcaceae UCG-002 were observed. These changes indicate the adaptation of the piglets to a cereal-based diet rich in oligosaccharides and starch. Our results also show that the farm can have a significant impact in such a process, evidencing the influence of different environments and rearing systems on the gut microbiota development of the young piglet. Differences between farms were more noticeable after weaning than during lactation with changes in alpha and beta biodiversity and specific taxa. The analysis of such differences suggests that piglets receiving intramuscular amoxicillin (days 2-5 of life) and being offered an acidifying rehydrating solution (Alpha farm in Trial 1) have a greater alpha diversity and more abundant Lactobacillus population. Moreover, the only farm that did not offer any rehydrating solution (Foxtrot farm in Trial 2) showed a lower alpha diversity (day 2 of life) and increased abundance of Enterobacteriaceae (both at 2 and 21 days). The use of in-feed antibiotics in the sows was also associated with structural changes in the piglets' gut ecosystem although without changes in richness or diversity. Significant shifts could be registered in different microbial groups, particularly lower abundances of Fusobacterium in those piglets from medicated sows.

CONCLUSIONS

In conclusion, during the first weeks of life, the pig microbiota showed a relevant succession of microbial groups towards a more homogeneous and stable ecosystem better adapted to the solid dry feed. In this relevant early-age process, the rearing conditions, the farm environment, and particularly the antimicrobial use in piglets and mothers determine changes that could have a relevant impact on gut microbiota maturation. More research is needed to elucidate the relative impact of these farm-induced early life-long changes in the growing pig.

Impact of ileal indigestible protein on fecal nitrogen excretion and fecal microbiota may be greater compared with total protein concentration of diets in growing pigs

In the current study, we hypothesized that an increase in dietary ileal indigestible protein concentration induces an increase in hindgut nitrogen utilization and nitrogen excretion and a shift in fecal microbiota in growing pigs, when compared to pigs given a high total protein diet. Three diets were prepared: 1) standard protein diet based on corn and soybean meal, 2) high-indigestible protein diet in which autoclaved, low-digestible soybean meal replaced soybean meal in the first diet, and 3) high protein diet where the inclusion rate of soybean meal was greater than that of the other diets. The 3 diets were fed to 18 barrows that were fitted with T-cannula at the ileo-cecal junction (initial body weight = 63.4 ± 8.0 kg) in a randomized complete block design with body weight as a blocking factor. Pigs were individually housed in pens and the experiment lasted for 23 d. On days 7 and 21, fecal samples were collected by rectal massage for microbiota analysis. Grab samples of feces were collected on days 20 and 21, and ileal digesta were collected on days 22 and 23 for the determination of energy and nitrogen utilization. Lower apparent ileal digestibility of nitrogen in the high-indigestible protein diet containing autoclaved soybean meal resulted in greater ileal indigestible nitrogen concentration (P < 0.05). Apparent total tract digestibility of nitrogen was lower (P < 0.05), and correspondingly nitrogen concentration and daily fecal nitrogen output were greater (P < 0.05) in the high-indigestible protein diet compared with the other diets. Apparent post-ileal digestibility and hindgut disappearance of nitrogen and gross energy were the greatest (P < 0.05) in the high protein diet, whereas a statistical difference was not observed in those variables between the standard protein diet and the high-indigestible protein diet. Beta diversity metrics of feces in the high-indigestible protein diet on day 21 were different (q < 0.05) from those in the other two diets, which indicates a shift in microbial communities. According to the results of the DESeq2, the direction of microbiota shift induced by the high-indigestible protein diet may have reduced fiber utilization in the hindgut. In conclusion, an increase in dietary ileal indigestible protein concentration increased fecal nitrogen excretion and shifted fecal microbial communities but did not increase nitrogen utilization in the hindgut.

Time-course effects of different fiber-rich ingredients on energy values, microbiota composition and SCFA profile in growing pigs

This study was to investigate time-course effects of different types of dietary fiber on the energy values, fecal microbiota and short-chain fatty acid (SCFA) concentration in growing pigs. A total of 24 barrows (initial body weight, 19.8 ± 0.5 kg) were assigned to 4 dietary treatments based on body weight (BW) in a completely randomized design, including a basal diet (CON) and 3 fiber-rich diets replacing corn, soybean meal and soybean oil in the CON diet with 20% sugar beet pulp (SBP), defatted rice bran (DFRB) or soybean hull (SBH), respectively. Fresh feces were sampled on d 7, 14 and 21, followed by 5 d total feces and urine collections. The results showed that there were no differences in DE and ME between any of the fiber ingredients on d 7, 14 or 21. However, fiber inclusion decreased the DE and ME of the diet (P < 0.05) regardless of the time effect. Principal coordinate analysis (PCoA) revealed distinctly different microbial communities on the DFRB diet and SBH diet across different times (P < 0.05) and the fecal microbiota of the 4 diet groups demonstrated notably distinct clusters at each time point (P < 0.05). With adaptation time increased from 7 to 21 d, cellulose-degrading bacteria and SCFA-producing bacteria (e.g., Ruminococcaceae _UCG-014, Rikenellaceae _RC9_gut_group and Bifidobacterium) increased in the fiber inclusion diets, and pathogenic genera (e.g., Streptococcus and Selenomonas) were increased in the basal diet (P < 0.05). Furthermore, the gut microbiota of growing pigs adapted more easily and quickly to the SBP diet compared to the DFRB diet, as reflected by the concentration of propionate, butyrate, isovalerate and total SCFA which increased with time for growing pigs fed the DFRB diet (P < 0.05). Collectively, our results indicated at least 7 d adaptation was required to evaluate the energy values of fiber-rich ingredients, as the hindgut microbiota of growing pigs may need more time to adapt to a high fiber diet, especially for insoluble dietary fiber.

Identification of Gut Microbiota Affecting Fiber Digestibility in Pigs

Dietary fiber plays an important role in porcine gut health and welfare. Fiber is degraded by microbial fermentation in the intestine, and most gut microbiota related to fiber digestibility in pigs are worth pursuing. The aim of this study was to identify gut microbiota associated with the apparent total tract digestibility (ATTD) of neutral detergent fiber (NDF) and of acid detergent fiber (ADF) in pigs. Large phenotypic variations in the ATTD of NDF and of ADF were separately found among 274 Suhuai pigs. Microbial community structures were significantly different between high and low fiber digestibility groups. Fourteen genera separately dominated the communities found in the high ATTD (H-AD) of NDF and ADF samples and were in very low abundance in the low ATTD (L-AD) of NDF and ADF samples. In conclusion, norank_f__Bacteroidales_S24-7_group (p < 0.05), Ruminococcaceae_UCG-005 (p < 0.05), unclassified_f__Lachnospiraceae (p < 0.05), Treponema_2 (p < 0.01), and Ruminococcaceae_NK4A214_group (p < 0.01) were the main genera of gut microbiota affecting the ATTD of NDF in pigs. Christensenellaceae_R-7_group (p < 0.01), Treponema_2 (p < 0.05), Ruminococcaceae_NK4A214_group (p < 0.05), Ruminococcaceae_UCG-002 (p < 0.05), and [Eubacterium]_coprostanoligenes_group (p < 0.05) were the main genera of gut microbiota affecting the ATTD of ADF in pigs. The most important functions of the above different potential biomarkers were: carbohydrate transport and metabolism, general function prediction only, amino acid transport and metabolism, cell wall/membrane/envelope biogenesis, translation, transcription, replication, energy production and conversion, signal transduction mechanisms, and inorganic ion transport and metabolism. The most important metabolic pathways of the above different potential biomarkers were: membrane transport, carbohydrate metabolism, amino acid metabolism, replication and repair, translation, cell motility, energy metabolism, poorly characterized, nucleotide metabolism, metabolism of cofactors and vitamins, and cellular processes and signaling.

Dietary Supplementation of Limosilactobacillus mucosae LM1 Enhances Immune Functions and Modulates Gut Microbiota Without Affecting the Growth Performance of Growing Pigs

Limosilactobacillus mucosae LM1 (LM1) is previously isolated from the intestine of piglets, but its potential as a probiotic supplement has not yet been assessed in growing pigs. In this study, we analyzed the probiotic effect of LM1 on the growth performance, apparent total tract digestibility (ATTD) of nutrients, immune properties, intestinal morphology, and gut microbiota and their metabolites in growing pigs. The experiment included 145 Duroc × (Landrace × Yorkshire) pigs (average body weight: 21.21 ± 1.14 kg) distributed into five treatment groups. The pigs were fed either a control diet (CON), or the control diet supplemented with incremental doses of LM1, namely low-dose LM1 (LL, 8.3 × 108 CFU/kg), moderate-low dose LM1 (ML, 4.2 × 109 CFU/kg), moderate-high dose LM1 (MH, 8.3 × 109 CFU/kg), and high-dose LM1 (HH, 2.1 × 1010 CFU/kg) for 42 d. On d 42, 12 pigs from each of the CON and MH groups were slaughtered. The results indicated that the ATTD of nitrogen (N, P = 0.038) was improved with MH supplementation. In addition, increasing dose of LM1 improved the immune response in pigs by reducing serum pro-inflammatory cytokines (interleukin-1β and tumor necrosis factor-alpha) and increasing anti-inflammatory cytokines (interleukin-10). Pigs fed with MH LM1 also had higher jejunal villus height and ileal villus height: crypt depth ratio, demonstrating improved intestinal morphology. Moreover, moderate-high LM1 supplementation enriched SCFA-producing taxa such as Lactobacillus, Holdemanella, Peptococcus, Bifidobacterium, Eubacterium_hallii_group, and Lachnospiraceae_AC2044_group, which correlated positively with increased fecal levels of butyrate and iso-valerate. These results strongly suggest the probiotic potential of LM1 on growing pigs. Overall, the current study provides insights on the use of L. mucosae LM1 as a novel livestock probiotic to improve pig gut health.

Genetic relationships between efficiency traits and gut microbiota traits in growing pigs fed a conventional or a high fiber diet

In pigs, the gut microbiota composition plays a major role in the process of digestion, but is influenced by many external factors, especially diet. To be used in breeding applications, genotype by diet interactions on microbiota composition have to be quantified, as well as their impact on genetic covariances with feed efficiency (FE) and digestive efficiency (DE) traits. This study aimed at determining the impact of an alternative diet on variance components of microbiota traits (genera and alpha diversity indices) and estimating genetic correlations between microbiota and efficiency traits for pigs fed a conventional (CO) or a high-fiber (HF) diet. Fecal microbes of 812 full-siblings fed a CO diet and 752 pigs fed the HF diet were characterized at 16 weeks of age by sequencing the V3-V4 region of the 16S rRNA gene. A total of 231 genera were identified. Digestibility coefficients of nitrogen, organic matter, and energy were predicted analyzing the same fecal samples with near infrared spectrometry. Daily feed intake, feed conversion ratio, residual feed intake and average daily gain (ADG) were also recorded. The 71 genera present in more than 20% of individuals were retained for genetic analyses. Heritability (h²) of microbiota traits were similar between diets (from null to 0.38 ± 0.12 in the CO diet and to 0.39 ± 0.12 in the HF diet). Only three out of the 24 genera and two alpha diversity indices with significant h² in both diets had genetic correlations across diets significantly different from 0.99 (P < 0.05), indicating limited genetic by diet interactions for these traits. When both diets were analyzed jointly, 59 genera had h² significantly different from zero. Based on the genetic correlations between these genera and ADG, FE, and DE traits, three groups of genera could be identified. A group of 29 genera had abundances favorably correlated with DE and FE traits, 14 genera were unfavorably correlated with DE traits, and the last group of 16 genera had abundances with correlations close to zero with production traits. However, genera abundances favorably correlated with DE and FE traits were unfavorably correlated with ADG, and vice versa. Alpha diversity indices had correlation patterns similar to the first group. In the end, genetic by diet interactions on gut microbiota composition of growing pigs were limited in this study. Based on this study, microbiota-based traits could be used as proxies to improve FE and DE in growing pigs.

Trace amounts of antibiotic altered metabolomic and microbial profiles of weaned pigs infected with a pathogenic E. coli

Background

Our previous study has shown that supplementation of trace amounts of antibiotic exacerbated the detrimental effects of enterotoxigenic E. coli (ETEC) infection and delayed the recovery of pigs that may be associated with modified metabolites and metabolic pathways. Therefore, the objective of this study was to explore the impacts of trace levels of antibiotic (carbadox) on host metabolic profiles and colon microbiota of weaned pigs experimentally infected with ETEC F18.

Results

The multivariate analysis highlighted a distinct metabolomic profile of serum and colon digesta between trace amounts of antibiotic (TRA; 0.5 mg/kg carbadox) and label-recommended dose antibiotic (REC; 50 mg/kg carbadox) on d 5 post-inoculation (PI). The relative abundance of metabolomic markers of amino acids, carbohydrates, and purine metabolism were significantly differentiated between the TRA and REC groups (q < 0.2). In addition, pigs in REC group had the highest (P < 0.05) relative abundance of Lactobacillaceae and tended to have increased (P < 0.10) relative abundance of Lachnospiraceae in the colon digesta on d 5 PI. On d 11 PI, pigs in REC had greater (P < 0.05) relative abundance of Clostridiaceae compared with other groups, whereas had reduced (P < 0.05) relative abundance of Prevotellaceae than pigs in control group.

Conclusions

Trace amounts of antibiotic resulted in differential metabolites and metabolic pathways that may be associated with its slow responses against ETEC F18 infection. The altered gut microbiota profiles by label-recommended dose antibiotic may contribute to the promotion of disease resistance in weaned pigs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-022-00703-5.

Dietary Fiber Influences Bacterial Community Assembly Processes in the Gut Microbiota of Durco × Bamei Crossbred Pig

Several studies have shown that dietary fiber can significantly alter the composition and structure of the gut bacterial community in humans and mammals. However, few researches have been conducted on the dynamics of the bacterial community assembly across different graded levels of dietary fiber in different gut regions. To address this, 24 Durco × Bamei crossbred pigs were randomly assigned to four experimental chows comprising graded levels of dietary fiber. Results showed that the α-and β-diversity of the bacterial community was significantly different between the cecum and the jejunum. Adding fiber to the chow significantly increased the α-diversity of the bacterial community in the jejunum and cecum, while the β-diversity decreased. The complexity of the bacterial network increased with the increase of dietary fiber in jejunal content samples, while it decreased in cecal content samples. Furthermore, we found that stochastic processes governed the bacterial community assembly of low and medium dietary fiber groups of jejunal content samples, while deterministic processes dominated the high fiber group. In addition, deterministic processes dominated all cecal content samples. Taken together, the variation of gut community composition and structure in response to dietary fiber was distinct in different gut regions, and the dynamics of bacterial community assembly across the graded levels of dietary fiber in different gut regions was also distinct. These findings enhanced our knowledge on the bacterial community assembly processes in gut ecosystems of livestock.

Analysing microbiome intervention design studies: Comparison of alternative multivariate statistical methods

The diet plays a major role in shaping gut microbiome composition and function in both humans and animals, and dietary intervention trials are often used to investigate and understand these effects. A plethora of statistical methods for analysing the differential abundance of microbial taxa exists, and new methods are constantly being developed, but there is a lack of benchmarking studies and clear consensus on the best multivariate statistical practices. This makes it hard for a biologist to decide which method to use. We compared the outcomes of generic multivariate ANOVA (ASCA and FFMANOVA) against statistical methods commonly used for community analyses (PERMANOVA and SIMPER) and methods designed for analysis of count data from high-throughput sequencing experiments (ALDEx2, ANCOM and DESeq2). The comparison is based on both simulated data and five published dietary intervention trials representing different subjects and study designs. We found that the methods testing differences at the community level were in agreement regarding both effect size and statistical significance. However, the methods that provided ranking and identification of differentially abundant operational taxonomic units (OTUs) gave incongruent results, implying that the choice of method is likely to influence the biological interpretations. The generic multivariate ANOVA tools have the flexibility needed for analysing multifactorial experiments and provide outputs at both the community and OTU levels; good performance in the simulation studies suggests that these statistical tools are also suitable for microbiome data sets.

Effects of Partially Hydrolyzed Guar Gum Supplementation on the Fecal Microbiotas of Piglets

Probiotics and prebiotics have become viable alternatives of growth-promoting antimicrobials in animal production. Here, we tested partially hydrolyzed guar gum (PHGG) as a possible prebiotic for piglets in the commercial farm. Five hundred and ninety-four piglets were used for the experiments, with 293 given a normal pig feed (control), while the rest the feed plus 0.06% (w/w) of PHGG (PHGG). One and three months post-PHGG supplementation, fecal samples were collected from randomly selected 20 piglets in each group and analyzed for microbiota and organic acid concentrations. Notably, the abundance of Streptococcus, and unclassified Ruminococcaceae were lower (p < 0.05) in PHGG than in control, one-month post-supplementation. Lactobacillus and Prevotella were higher (p < 0.05), while Streptococcus was lower (p < 0.05), in PHGG than in control, three months post-supplementation. The concentrations of acetate, propionate, and butyrate were greater in PHGG than in control, three months post-supplementation. Finally, PHGG grew faster and had fewer deaths until slaughter time (p < 0.05), than control. We concluded that PHGG not only was an effective prebiotic to alter gut microbiota of weanling piglets but also can possibly promote body weight accretion and health.

Review: Can early-life establishment of the piglet intestinal microbiota influence production outcomes?

The gastrointestinal tract microbiota is involved in the development and function of many body processes. Studies demonstrate that early-life microbial colonisation is the most important time for shaping intestinal and immune development, with perturbations to the microbiota during this time having long-lasting negative implications for the host. Piglets face many early-life events that shape the acquisition and development of their intestinal microbiota. The pork industry has a unique advantage in that the producer has a degree of control over what piglets are exposed to, providing conditions that allow for optimum piglet growth and development. An influx of publications within this area has occurred in recent times and with this, interest surrounding its application in pork production has increased. However, it can be difficult to distinguish which research is of most relevance to industry in terms of delivering repeatable and reliable production outcomes. In this review, we describe the literature surrounding research within pigs, predominantly during the preweaning period that has either provided solutions to industry problems or is generating information targeted at addressing relevant industry issues, with the focus being on studies demonstrating causation where possible. This review will provide a basis for the development of new studies targeted at understanding how to better support initial intestinal microbiota colonisation in order to improve piglet health and survival.

Variation in faecal digestibility values related to feed efficiency traits of grower-finisher pigs

Providing pigs a diet that matches their nutrient requirements involves optimizing the diet based on the nutrient digestibility values of the considered feed ingredients. Feeding the same quantity of a diet to pigs with similar BW but with different requirements, however, can result in a different average daily gain (ADG) and backfat thickness (BF) between pigs. Digestibility may contribute to this variation in efficiency. We investigated variation in feed efficiency traits in grower-finisher pigs associated with variation in faecal digestibility values, independent of feed intake at the time of measuring faecal digestibility. Considered traits were ADG, average daily feed intake (ADFI), feed conversion ratio (FCR), BF and residual feed intake (RFI). Feed intake, BW, and BF data of one hundred and sixty three-way crossbreed grower-finisher pigs (eighty female and eighty male) were collected during two phases, from day 0 of the experiment (mean BW 23 kg) till day 56 (mean BW 70 kg) and from day 56 to slaughter (mean BW 121 kg). Pigs were either fed a diet based on corn/soybean meal or a more fibrous diet based on wheat/barley/by-products, with titanium dioxide as indigestible marker. Faecal samples of one hundred and five pigs were collected on the day before slaughter and used to determine apparent faecal digestibility of DM, ash, organic matter (OM), CP, crude fat (CFat), crude fibre (CF), and to calculate the digestibility of nonstarch polysaccharides (NSPs) and energy (E). The effects of diet, sex and covariate feed intake at sampling (FIs) on faecal digestibility values were estimated and were significant for all except for CFat. Faecal digestibility values of each individual pig determined at the day before slaughter, corrected for diet, sex and FIs, were used to estimate their association with ADG, ADFI, FCR, BF, and RFI. In the first phase, a one percent unit increase in faecal digestibility of DM, ash, OM, E, CP, CFat, CF, NSP, and Ash individually was related to 0.01-0.03 unit reduction in FCR and 6-23 g/day reduction in RFI. A unit increase in CP digestibility was related to 0.1 mm increase in BF and 10 g/day increase in ADG. In the second phase, a one percent unit increase in faecal digestibility of DM, CP and Ash was related to a decrease of 16-20 g/day in RFI. In conclusion, the relationship between variation in feed efficiency traits and faecal digestibility values is different across the developmental stages of a pig.

Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigs

BACKGROUND

Phenotypic variability for productive and meat quality traits has been largely studied in Iberian pigs, especially in genetic selection and nutritional experiments. Complex interactions among genetic background, diet composition and gut microbiota hinder the correct assessment of each factor's contribution on phenotypes. In order to disentangle these interactions, we evaluated changes in gut microbiota composition comparing 48 Iberian and Duroc pigs fed diets with different energy source (standard diet with carbohydrates vs sunflower oil-enriched diet with high oleic acid content).

RESULTS

A higher richness was observed for Iberian pigs (p < 0.05) and compositional analysis was applied for beta-diversity, differential abundance and pairwise log-ratio analyses. We found significant differences in overall microbiota composition between breeds, and also between diets inside breeds, to a lesser extent. Differential abundance analysis revealed that Duroc animals have more proportion of Actinobacteria and Prevotella, while Iberian replace those microorganisms with other more variable taxa. According to dietary differences, high-oleic fed animals were richer in Prevotella. We also found microbial ratios capable of separating animals by breeds and diets, mostly related to Actinobacteria.

CONCLUSION

This study reveals that both genetic background and diet composition might have a relevant impact in gut microbiota composition. The application of compositional data analysis has facilitated the identification of microorganisms and ratios as possibly related to metabolic changes due to genetic background and, to a lower extent, to dietary changes. This may lead to a relevant progress in the knowledge of interactions between pig genetics, environment and gut microbiota.

Faecal concentrations of ceftiofur metabolites in finisher pigs administered intramuscularly with ceftiofur

The objective of this study was to determine the effects of dietary fibre level and source on faecal ceftiofur metabolites concentrations after intramuscular administration of therapeutic ceftiofur hydrochloride in finisher pigs. Pens of finisher pigs (n = 36), with an equal number of barrows and gilts, were randomly assigned to 1 of 3 dietary treatment groups: basal diet composed of corn grain and soy bean meal with no supplement and formulated to contain 8.7% neutral detergent fibre (NDF), supplemented with 20% distillers dried grains with solubles (a byproduct of the ethanol production from corn grain) formulated to contain 13.6% NDF, primarily insoluble fibre or supplemented with 14.5% sugar beet pulp formulated to contain 13.6% NDF. Faecal samples were collected 6–8 hr after ceftiofur injection from treated and untreated pen‐mate pigs on days 1 and 3 of the 3‐day treatment regimen. Faecal concentrations of ceftiofur metabolites, including the major metabolite, desfuroylceftiofur, were analysed by reverse‐phase high pressure liquid chromatography with ultraviolet detection. Overall, the faecal concentrations of ceftiofur metabolites did not differ significantly between the dietary treatments. The mean concentrations of metabolites tended to be lower (p = .1) on day 3 compared to day 1 of the 3‐day treatment regimen. Faecal concentrations of metabolites were not affected by the gender of the finisher pigs. The concentrations of ceftiofur metabolites in the faeces are likely reflective of the microbial activity in the hindgut. Our data suggest that the fibre level and source used in the study did not affect the faecal concentrations of ceftiofur metabolites.

The fecal microbiota of piglets during weaning transition and its association with piglet growth across various farm environments

This study describes the fecal microbiota from piglets reared in different living environments during the weaning transition, and presents the characteristics of microbiota associated with good growth of piglets after weaning. Fecal samples were collected pre- (d26) and post-weaning (d35) from 288 male piglets in 16 conventional indoor commercial farms located in the West of France. The changes one week after weaning on the most abundant microbial families was roughly the same in all farms: alpha diversity increased, the relative abundance of Bacteroidaceae (-61%), Christensenellaceae (-35%), Enterobacteriaceae (-42%), and Clostridiaceae (-32%) decreased, while the relative abundance of Prevotellaceae (+143%) and Lachnospiraceae (+21%) increased. Among all the collected samples, four enterotypes that were ubiquitous in all farms were identified. They could be discriminated by their respective relative abundances of Prevotella, Faecalibacterium, Roseburia, and Lachnospira, and likely corresponded to a gradual maturational shift from pre- to post-weaning microbiota. The rearing environment influenced the frequency of enterotypes, as well as the relative abundance of 6 families at d26 (including Christensenellaceae and Lactobacillaceae), and of 21 families at d35. In all farms, piglets showing the highest relative growth rate during the first three weeks after weaning, which were characterized as more robust, had a higher relative abundance of Bacteroidetes, a lower relative abundance of Proteobacteria, and showed a greater increase in Prevotella, Coprococcus, and Lachnospira in the post-weaning period. This study revealed the presence of ubiquitous enterotypes among the farms of this study, reflecting maturational stages of microbiota from a young suckling to an older cereal-eating profile. Despite significant variation in the microbial profile between farms, piglets whose growth after weaning was less disrupted were, those who had reached the more mature phenotype characterized by Prevotella the fastest.

Measures Matter-Determining the True Nutri-Physiological Value of Feed Ingredients for Swine

Many types of feed ingredients are used to provide energy and nutrients to meet the nutritional requirements of swine. However, the analytical methods and measures used to determine the true nutritional and physiological ("nutri-physiological") value of feed ingredients affect the accuracy of predicting and achieving desired animal responses. Some chemical characteristics of feed ingredients are detrimental to pig health and performance, while functional components in other ingredients provide beneficial health effects beyond their nutritional value when included in complete swine diets. Traditional analytical procedures and measures are useful for determining energy and nutrient digestibility of feed ingredients, but do not adequately assess their true physiological or biological value. Prediction equations, along with ex vivo and in vitro methods, provide some benefits for assessing the nutri-physiological value of feed ingredients compared with in vivo determinations, but they also have some limitations. Determining the digestion kinetics of the different chemical components of feed ingredients, understanding how circadian rhythms affect feeding behavior and the gastrointestinal microbiome of pigs, and accounting for the functional properties of many feed ingredients in diet formulation are the emerging innovations that will facilitate improvements in precision swine nutrition and environmental sustainability in global pork-production systems.

Influence of Different Herbal-Mix Feed Additives on Serological Parameters, Tibia Bone Characteristics and Gut Morphology of Growing Pigs

A sixteen-week study was carried out in order to investigate the effects of different herbal-mix feed additives (Moringa, Basil and Neem) on serological parameters, tibia bone characteristics and gut morphology of growing pigs. Eighty-one Large White breed of pigs with a mean weight of 15.35 ± 1.07 were grouped on weight equalization basis into three treatments with 9 replicates per treatment and 3 pigs per replicate in a completely randomized design. Pigs on treatment 1 were fed a ration without integration of herbal-mix feed additives, those in treatments 2 and 3 were offered a diet that contained moringa-basil leaf meal and neem-basil leaf meal respectively. Blood samples were collected from the experimental pigs on the 12th week of the study for the determination of serum levels, while 1 pig from each replicate group whose weight was close to the mean replicate weight was chosen at the end of the study, fasted for 12 hours, sacrificed and the small intestine and left tibia bone were harvested and used for gut and bone morphology evaluation. These data generated from the study were subjected to a 1-way analysis of variance (ANOVA). The results indicated that herbal-mix feed additives influenced some of the serological parameters, i.e., globulin, glucose, total cholesterol, high- and low-density lipoproteins, and aspartate aminotransferase. These parameters decreased with integration of different herbal-mix in the pigs’ diets except high density lipoprotein that increased statistically. The tibia characteristics such as tibia breaking strength, medial thickness and lateral thickness were also positively impacted by the dietary inclusion of the herbal-mix. Likewise, the villus height of the jejunum was positively enhanced by dietary inclusion of the herbal-mix feed additives. This study concluded that herbal-mix feed additives can be utilized in pigs’ nutrition in enhancing some serological parameters, tibia bone and gut characteristics of growing pigs.

Effects of Substitution of Corn with Ground Brown Rice on Growth Performance, Nutrient Digestibility, and Gut Microbiota of Growing-Finishing Pigs

Simple Summary

Corn is the main feed ingredient used in swine diets as an energy source due to its abundant production and nutrient contents. In South Korea, most of the corn for animal diets depends on import from other countries—more than 7.5 million tons per year. Thus, there is a need to find alternative ingredients to substitute corn in pig diets. Although there are variations depending on the degree of milling, brown rice has similar or better nutrient contents compared to corn. In addition, it is known to have excellent digestibility due to its smaller starch structure and granule size and less non-starch polysaccharides and anti-nutritional factors than corn. As a result of evaluating the effects of replacing corn with brown rice in pig diets, changes in gut microbiota were observed when corn was replaced with brown rice for a long time, but there were no differences on growth performance and carcass characteristics. Therefore, it has been confirmed that brown rice can replace corn in swine diets and the use of brown rice as a pig feed ingredient may be the basis for increasing feed self-sufficiency and enabling a stable feed supply.

Abstract

The present study was conducted to evaluate the effects of replacing corn with brown rice on growth performance, nutrient digestibility, carcass characteristics, and gut microbiota of growing and finishing pigs. A total of 100 growing pigs (23.80 ± 2.96 kg BW; 10 weeks of age) were randomly allotted to 4 dietary treatments (5 pigs/pen; 5 replicates/treatment) in a randomized complete block design (block = BW) as follows: corn-soybean meal basal diet (CON) and replacing corn with 50% (GBR50), 75% (GBR75), and 100% (GBR100) of ground brown rice. Each trial phase was for 6 weeks. During the growing period, there were no differences on growth performance and nutrient digestibility among dietary treatments. Similarly, no differences were found on growth performance, nutrient digestibility, and carcass characteristics of pigs during the finishing period among dietary treatments. As a result of the beta diversity analysis, microbial populations were not clustered between CON and GBR100 during the growing phase, but clustered into two distinct groups of CON and GBR100 during the finishing phase. In conclusion, brown rice can be added to the diets of growing-finishing pigs by replacing corn up to 100% without negatively affecting growth performance of the pigs; additionally, this may have an effect on changes in pig intestinal microbiota if continued for a long time.

Xylanase modulates the microbiota of ileal mucosa and digesta of pigs fed corn-based arabinoxylans likely through both a stimbiotic and prebiotic mechanism

The experimental objective was to characterize the impact of insoluble corn-based fiber, xylanase, and an arabinoxylan-oligosaccharide on ileal digesta and mucosa microbiome of pigs. Three replicates of 20 gilts were blocked by initial body weight, individually-housed, and assigned to 1 of 4 dietary treatments: a low-fiber control (LF), a 30% corn bran high-fiber control (HF), HF+100 mg/kg xylanase (HF+XY), and HF+50 mg/kg arabinoxylan oligosaccharide (HF+AX). Gilts were fed their respective treatments for 46 days. On day 46, pigs were euthanized and ileal digesta and mucosa were collected. The V4 region of the 16S rRNA was amplified and sequenced, generating a total of 2,413,572 and 1,739,013 high-quality sequences from the digesta and mucosa, respectively. Sequences were classified into 1,538 mucosa and 2,495 digesta operational taxonomic units (OTU). Hidden-state predictions of 25 enzymes were made using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUST2). Compared to LF, HF increased Erysipelotrichaceae_UCG-002, and Turicibacter in the digesta, Lachnospiraceae_unclassified in the mucosa, and decreased Actinobacillus in both (Q<0.05). Relative to HF, HF+XY increased 19 and 14 of the 100 most abundant OTUs characterized from digesta and mucosa, respectively (Q<0.05). Notably, HF+XY increased the OTU_23_Faecalibacterium by nearly 6 log2-fold change, compared to HF. Relative to HF, HF+XY increased genera Bifidobacterium, and Lactobacillus, and decreased Streptococcus and Turicibacter in digesta (Q<0.05), and increased Bifidobacterium and decreased Escherichia-Shigella in the mucosa (Q<0.05). Compared to HF, HF+AX increased 5 and 6 of the 100 most abundant OTUs characterized from digesta and mucosa, respectively, (Q<0.05), but HF+AX did not modulate similar taxa as HF+XY. The PICRUST2 predictions revealed HF+XY increased gene-predictions for enzymes associated with arabinoxylan degradation and xylose metabolism in the digesta, and increased enzymes related to short-chain fatty acid production in the mucosa. Collectively, these data suggest xylanase elicits a stimbiotic and prebiotic mechanism.

Changes in Faecal Microbiota Profiles Associated With Performance and Birthweight of Piglets

The gastrointestinal tract microbiota interacts with the host to modulate metabolic phenotype. This interaction could provide insights into why some low birthweight pigs can exhibit compensatory growth whilst others remain stunted. This study aimed to identify microbiota markers associated with birthweight [low birthweight (n = 13) or normal birthweight pigs (n = 13)] and performance ["good" or "poor" average daily gain (ADG) class]. Furthermore, the study determined whether the taxonomic markers were longitudinal, or time point specific in their ability to identify low birthweight pigs who could exhibit compensatory growth. Faecal samples were collected and liveweight recorded at 10 different time points from birth to 56 days of age. No consistent associations between birthweight, performance and gut microbiota were found across all time points. However, there was a significant (P < 0.05) effect of birthweight on microbiota richness at 21, 27, 32 and 56 days of age. Significant differences (P < 0.05) in genera abundance according to birthweight and performance were also identified. Low birthweight pigs had a significantly (P < 0.05) lower abundance of Ruminococcaceae UCG-005, but a significantly (P < 0.05) higher abundance of Ruminococcaceae UCG-014 on days 21 and 32, respectively. Piglets classified as having a "good" ADG class had a significantly (P < 0.05) higher abundance of Lactobacillus, unclassified Prevotellaceae and Ruminococcaceae UCG-005 on days 4, 8 and 14, respectively. Furthermore, Ruminococcaceae UCG-005 was significantly more abundant at 14 days of age in normal birthweight pigs with a "good" ADG class compared to those classified as "poor." The results of this study indicate that there are time point-specific differences in the microbiota associated with birthweight and performance, corresponding to the period in which solid feed intake first occurs. Identifying early-life microbiota markers associated with performance emphasises the importance of the neonatal phase when considering intervention strategies aimed at promoting performance.

Impact of increasing the levels of insoluble fiber and on the method of diet formulation measures of energy and nutrient digestibility in growing pigs

The objective of this study was to determine the differences in response to distillers dried grains with solubles (DDGS) level under constant nutrient or floating nutrient concentrations. A total of 21 ileal-cannulated gilts (33.1 ± 0.4 kg body weight) were randomly allotted to one of seven dietary treatments in a 3-period incomplete Latin square design (n = 9). Treatments consisted of a 0% DDGS basal diet, plus diets containing 15%, 30%, or 45% DDGS. Diets were formulated using one of two different formulation methods: 1) constant nutrient (CNU) where nutrients were held equal to the basal diet or 2) constant ingredients (CIN) where DDGS were added at the expense of corn and all other ingredients remained constant, so nutrient levels were allowed to "float." Chromic oxide was added to the diets at 0.5% as an indigestible marker. Increasing the level of DDGS decreased the apparent ileal digestibility (AID) of dry matter (DM), gross energy (GE), starch, dispensable amino acids (AA), and fiber components (P < 0.050). The decrease in the AID of Lys, Met, Thr, and Trp was more pronounced under CNU compared with the CIN formulation method (P < 0.050). The decrease in the AID of hemicellulose was less pronounced under CNU compared with the CIN formulation method (P = 0.045). There was a DDGS level × formulation method interaction for the AID of acid hydrolyzed ether extract (AEE; P = 0.015); for the CNU formulation method, increasing level of DDGS decreased the AID of AEE from 0% to 30% and remained similar from 30% to 45% DDGS, whereas the CIN had no effect on the AID of AEE. Increasing the level of DDGS decreased the apparent total tract digestibility (ATTD) of DM, GE, and fiber components (P < 0.050), except for acid detergent fiber, which was not affected. The decrease in the ATTD of insoluble dietary fiber and total dietary fiber was less pronounced under CNU compared with CIN (P < 0.050). The ATTD of AEE decreased for CNU compared with CIN (P < 0.010). In conclusion, increasing the insoluble fiber level in the form of DDGS decreased the digestibility of most dietary components, including DM, GE, starch, insoluble fiber, and AA. The CNU and CIN formulation methods are equivalent when evaluating the digestibilities of DM, GE, starch, crude protein, and AA (when they were not added in purified synthetic forms). Differences between CNU and CIN formulation methods were detected for the digestibility of insoluble fiber, fat, and essential AA (when added as crystalline AA).

High-level expression of an acidic thermostable xylanase in Pichia pastoris and its application in weaned piglets

An acidic thermostable xylanase (AT-xynA) which was stable at low pH and high temperature was considered to have great potential in animal feed. For large-scale production, AT-xynA activity was enhanced about 1-fold in Pichia pastoris by constructing a double-copy expression strain in this study. Furthermore, impacts of different AT-xynA levels on growth performance, nutrient digestibility, short-chain fatty acids, and bacterial community in weaned piglets were determined. Compared with the control group, ADFI and ADG were higher for the pigs fed 4,000 or 6,000 U/kg AT-xynA (P < 0.05). AT-xynA supplementation also significantly increased the digestibility of OM, GE, and DM (P < 0.05). AT-xynA supplementation increased the concentrations of acetate in ileal (P < 0.01) and cecal digesta (P < 0.05). Isobutyrate (P < 0.05) and valerate (P < 0.05) concentrations in colonic digesta also significantly increased compared with the control group. AT-xynA supplementation increased the abundance of Lactobacillus in the ileal, cecal, and colonic digesta of weaned piglets (P < 0.05). AT-xynA alleviated anti-nutritional effects of nonstarch polysaccharides (NSP) by preventing the growth of Pateurella and Leptotrichia in the ileum (P < 0.05). AT-xynA increased the abundance of NSP-degrading bacteria, such as Ruminococcaceae, Prevotella in the cecum and colon (P < 0.05). In summary, AT-xynA addition could improve the growth performance of weaned piglets by altering gut microbiota.

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

Simple Summary

Proper cooperation between digestive system microbiota and the host is an important issue in maintaining proper health condition, and—in the case of farm animals—production indices. In the case of pigs, microbiota significantly affect production parameters such as meat quality, growth rate or improvement of immune response to infections. Understanding of pig digestive system microbiota and factors affecting this is an important issue. This may enable improvement of animal performance and stabilization of microbiota during their growth, reducing the risk of metabolic or systemic diseases.

Abstract

The development of research methods and tools related to microbiome investigation, as well as widened knowledge and awareness concerning the significance of microorganisms inhabiting mammalian organisms, has led to an increasing popularity of studies in this field. This review paper presents some issues related to the swine microbiome, its development starting from an early age of life and its status in adult animals, as well as factors affecting the microbiome in pigs. Attention is paid to the role of probiotics and prebiotics as alternatives to antibiotics in the context of post-weaning diarrhea treatment, and to the role of microorganisms inhabiting the digestive tract of pigs in performance indices formation. In veterinary and pork production practice, understanding of the swine microbiome and its relationships with the host organism may be useful in the prevention of some diseases and also in improvement of performance results of animals.

In vitro prebiotic potential of agricultural by-products on intestinal fermentation, gut barrier and inflammatory status of piglets

The inclusion of fibre-rich ingredients in diets is one possible strategy to enhance intestinal fermentation and positively impact gut ecology, barrier and immunity. Nowadays, inulin-type fructans are used as prebiotics in the feed of piglets to manipulate gut ecology for health purposes. Likewise, some by-products could be considered as sustainable and inexpensive ingredients to reduce gut disorders at weaning. In the present study, chicory root and pulp, citrus pulp, rye bran and soya hulls were tested in a three-step in vitro model of the piglet's gastro-intestinal tract combining a pepsin-pancreatin hydrolysis (digestion), a dialysis step using cellulose membranes (absorption) and a colonic batch fermentation (fermentation). The fermentation kinetics, SCFA and microbiota profiles in the fermentation broth were assessed as indicators of prebiotic activity and compared with the ones of inulin. The immunomodulatory effects of fermentation supernatant (FS) were investigated in cultured intestinal porcine epithelial cells (IPEC-J2) by high-throughput quantitative PCR. Chicory root displayed a rapid and extensive fermentation and induced the second highest butyrate ratio after inulin. Citrus pulp demonstrated high acetate ratios and induced elevated Clostridium clusters IV and XIVa levels. Chicory root and pulp FS promoted the intestinal barrier integrity with up-regulated tight and adherens junction gene expressions in comparison with inulin FS. Chicory pulp FS exerted anti-inflammatory effects in cultured IPEC-J2. The novel approach combining an in vitro fermentation model with IPEC-J2 cells highlighted that both chicory root and pulp appear to be promising ingredients and should be considered to promote intestinal health at weaning.

Applicability of an Unmedicated Feeding Program Aimed to Reduce the Use of Antimicrobials in Nursery Piglets: Impact on Performance and Fecal Microbiota

Simple Summary

The need for a reduction in the use of antibiotics in livestock to safeguard their efficacy requires the development of alternatives. In this line, the use of alternative by-products or ingredients, with functional properties brings the opportunity to improve pig health and thus, reduce medicalization. Therefore, in the present study, we aimed to evaluate the impact of an alternative feeding program based on unmedicalized diets formulated with fibrous by-products and functional feed ingredients on performance and fecal microbiota of young pigs compared to a common weaner diet supplemented with antibiotics. The alternative feeding program could anticipate the gut development of young piglets, which at the end of the nursery period presented a fecal microbiota more similar to that found in fattening animals. Moreover, piglets in the unmedicalized diets showed a trend to reduce the course of diarrhea immediately after weaning. The alternative feeding program showed, however, a reduced growth efficiency during the nursery period that needs to be discussed in the frame of the costs-benefits analysis of reducing antibiotics.

Abstract

This study aimed to assess the impact of two different feeding programs, including or not antimicrobials, on gut microbiota development at early ages in commercial pigs. For this, 21-day-old weaned piglets were distributed into 12 pens (6 replicates with 26 pigs each) and fed ad libitum until fattening with: standard commercial formula with antibiotics and zinc oxide (2400 ppm) (AB), and alternative unmedicated feed formula (UN). Subsequently, the animals were moved to the fattening unit (F) receiving a common diet. Pigs were weighed, and feed consumption and diarrhea scores registered. Feces were collected on days 9 (pre-starter), 40 (starter) and 72 (fattening) post-weaning and microbial DNA extracted for 16S rDNA sequencing. Piglets fed UN diets had a worse feed efficiency (p < 0.05) than AB during nursery; however, UN pigs spent less time scouring after weaning (p = 0.098). The structure of fecal community evolved with the age of the animals (p = 0.001), and diet also showed to have a role, particularly in the starter period when UN microbiomes clustered apart from AB, resembling the ecosystems found in the fattening animals. Fibrolytic genera (Fibrobacter, Butyrivibrio, Christellansellaceae) were enriched in UN piglets whereas Lactobacillus characterized AB piglets (adjusted p < 0.05). Overall, this alternative feeding program could anticipate the gut development of piglets despite a lower feed efficiency compared to standard medicalized programs.

Bioregional Alterations in Gut Microbiome Contribute to the Plasma Metabolomic Changes in Pigs Fed with Inulin

Inulin (INU) is a non-digestible carbohydrate, known for its beneficial properties in metabolic disorders. However, whether and how gut microbiota in its regulation contributes to host metabolism has yet to be investigated. We conduct this study to examine the possible associations between the gut microbiota and circulating gut microbiota-host co-metabolites induced by inulin interventions. Plasma and intestinal site samples were collected from the pigs that have consumed inulin diet for 60 days. High-throughput sequencing was adopted for microbial composition, and the GC-TOF-MS-based metabolomics were used to characterize featured plasma metabolites upon inulin intervention. Integrated multi-omics analyses were carried out to establish microbiota-host interaction. Inulin consumption decreased the total cholesterol (p = 0.04) and glucose (p = 0.03) level in serum. Greater β-diversity was observed in the cecum and colon of inulin-fed versus that of control-fed pigs (p < 0.05). No differences were observed in the ileum. In the cecum, 18 genera were altered by inulin, followed by 17 in the colon and 6 in the ileum. Inulin increased propionate, and isobutyrate concentrations but decreased the ratio of acetate to propionate in the cecum, and increased total short fatty acids, valerate, and isobutyrate concentrations in the colon. Metabolomic analysis reveals that indole-3-propionic acid (IPA) was significantly higher, and the branched-chain amino acids (BCAA), L-valine, L-isoleucine, and L-leucine are significantly lower in the inulin groups. Mantel test and integrative analysis revealed associations between plasma metabolites (e.g., IPA, BCAA, L-tryptophan) and inulin-responsive cecal microbial genera. These results indicate that the inulin has regional effects on the intestine microbiome in pigs, with the most pronounced effects occurring in the cecum. Moreover, cecum microbiota plays a pivotal role in the modulation of circulating host metabolites upon inulin intervention.

Effect of chronic and acute heat challenges on fecal microbiota composition, production, and thermoregulation traits in growing pigs1,2

The present study aimed at investigating the impact of heat challenges on gut microbiota composition in growing pigs and its relationship with pigs’ performance and thermoregulation responses. From a total of 10 F1 sire families, 558 and 564 backcross Large White × Créole pigs were raised and phenotyped from 11 to 23 wk of age in temperate (TEMP) and in tropical (TROP) climates, respectively. In TEMP, all pigs were subjected to an acute heat challenge (3 wk at 29 °C) from 23 to 26 wk of age. Feces samples were collected at 23 wk of age both in TEMP and TROP climate (TEMP23 and TROP23 samples, respectively) and at 26 wk of age in TEMP climate (TEMP26 samples) for 16S rRNA analyses of fecal microbiota composition. The fecal microbiota composition significantly differed between the 3 environments. Using a generalized linear model on microbiota composition, 182 operational taxonomic units (OTU) and 2 pathways were differentially abundant between TEMP23 and TEMP26, and 1,296 OTU and 20 pathways between TEMP23 and TROP23. Using fecal samples collected at 23 wk of age, pigs raised under the 2 climates were discriminated with 36 OTU using a sparse partial least square discriminant analysis that had a mean classification error-rate of 1.7%. In contrast, pigs in TEMP before the acute heat challenge could be discriminated from the pigs in TEMP after the heat challenge with 32 OTU and 9.3% error rate. The microbiota can be used as biomarker of heat stress exposition. Microbiota composition revealed that pigs were separated into 2 enterotypes. The enterotypes were represented in both climates. Whatever the climate, animals belonging to the Turicibacter–Sarcina–Clostridium sensu stricto dominated enterotype were 3.3 kg heavier (P < 0.05) at 11 wk of age than those belonging to the Lactobacillus-dominated enterotype. This latter enterotype was related to a 0.3 °C lower skin temperature (P < 0.05) at 23 wk of age. Following the acute heat challenge in TEMP, this enterotype had a less-stable rectal temperature (0.34 vs. 0.25 °C variation between weeks 23 and 24, P < 0.05) without affecting growth performance (P > 0.05). Instability of the enterotypes was observed in 34% of the pigs, switching from an enterotype to another between 23 and 26 wk of age after heat stress. Despite a lower microbial diversity, the Turicibacter–Sarcina–Clostridium sensu stricto dominated enterotype was better adapted to heat stress conditions with lower thermoregulation variations.

Longitudinal Analysis of the Microbiota Composition and Enterotypes of Pigs from Post-Weaning to Finishing

The present study aimed at investigating the evolution of pigs’ fecal microbiota composition from post-weaning to finishing in a longitudinal analysis. The experiment was conducted on 160 Pietrain × (Large White × Landrace) castrated male and female pigs in two replicates. Feces were collected at 52, 99, 119, 140, and 154 days of age for further 16S rRNA sequencing to analyze the microbiota composition. Pig microbiota evolved strongly from 52 to 99 days of age with an increased abundance of Streptococcaceae and a decreased abundance of Lactobacillaceae. During the finishing stage, microbiota kept evolving at a slower rate. To link the community structure to the performances, the fecal samples were clustered into enterotypes sharing a similar bacterial composition. At 52 days, two enterotypes dominated either by Lactobacillus or by Prevotella–Sarcina were identified. They differed from the two enterotypes determined from 99 to 154 days which were dominated either by Lactobacillus or by Turicibacter–Clostridiumsensustricto. During this time period, 75% of the pigs switched enterotypes. The enterotypes were not related to differences in the overall growth or feeding performance. The enterotype definition was time-dependent and seemed to be related to the sex type at 99 days of age.

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.

Potential relevance of pig gut content transplantation for production and research

It is becoming increasingly evident that the gastrointestinal microbiota has a significant impact on the overall health and production of the pig. This has led to intensified research on the composition of the gastrointestinal microbiota, factors affecting it, and the impact of the microbiota on health, growth performance, and more recently, behavior of the host. Swine production research has been heavily focused on assessing the effects of feed additives and dietary modifications to alter or take advantage of select characteristics of gastrointestinal microbes to improve health and feed conversion efficiency. Research on faecal microbiota transplantation (FMT) as a possible tool to improve outcomes in pigs through manipulation of the gastrointestinal microbiome is very recent and limited data is available. Results on FMT in humans demonstrating the transfer of phenotypic traits from donors to recipients and the high efficacy of FMT to treat Clostridium difficile infections in humans, together with data from pigs relating GI-tract microbiota composition with growth performance has likely played an important role in the interest towards this strategy in pig production. However, several factors can influence the impact of FMT on the recipient, and these need to be identified and optimized before this tool can be applied to pig production. There are obvious inherent biosecurity and regulatory issues in this strategy, since the donor's microbiome can never be completely screened for all possible non-desirable microorganisms. However, considering the success observed in humans, it seems worth investigating this strategy for certain applications in pig production. Further, FMT research may lead to the identification of specific bacterial group(s) essential for a particular outcome, resulting in the development of banks of clones which can be used as targeted therapeutics, rather than the broader approach applied in FMT. This review examines the factors associated with the use of FMT, and its potential application to swine production, and includes research on using the pig as model for human medical purposes.