Host-Microbiota Interactions in Ileum and Caecum of Pigs Divergent in Feed Efficiency Contribute to Nutrient Utilization

The fecal microbiota of Holstein cows is heritable and genetically correlated to dairy performances

The fecal microbiota of ruminants constitutes a diversified community that has been phenotypically associated with a variety of host phenotypes, such as production and health. To gain a better understanding of the complex and interconnected factors that drive the fecal bacterial community, we have aimed to estimate the genetic parameters of the diversity and composition of the fecal microbiota, including heritabilities, genetic correlations among taxa, and genetic correlations between fecal microbiota features and host phenotypes. To achieve this, we analyzed a large population of 1,875 Holstein cows originating from 144 French commercial herds and routinely recorded for production, somatic cell score, and fertility traits. Fecal samples were collected from the animals and subjected to 16S rRNA gene sequencing, with reads classified into Amplicon Sequence Variants (ASVs). The estimated α- and β-diversity indices (i.e., Observed Richness, Shannon index, Bray-Curtis and Jaccard dissimilarity matrices) and the abundances of ASVs, genera, families and phyla, normalized by centered-log ratio (CLR), were considered as phenotypes. Genetic parameters were calculated using either univariate or bivariate animal models. Heritabilities estimates, ranging from 0.08 to 0.31 for taxa abundances and β-diversity indices, highlight the influence of the host genetics on the composition of the fecal microbiota. Furthermore, genetic correlations estimated within the microbial community and between microbiota features and host traits reveal the complex networks linking all components of the fecal microbiota together and to their host, thus strengthening the holobiont concept. By estimating the heritabilities of microbiota-associated phenotypes, our study quantifies the impact of the host genetics on the fecal microbiota composition. In addition, genetic correlations between taxonomic groups and between taxa abundances and host performance suggest potential applications for selective breeding to improve host traits or promote a healthier microbiota.

Knowledge graph-derived feed efficiency analysis via pig gut microbiota

Feed efficiency (FE) is essential for pig production, has been reported to be partially explained by gut microbiota. Despite an extensive body of research literature to this topic, studies regarding the regulation of feed efficiency by gut microbiota remain fragmented and mostly confined to disorganized or semi-structured unrestricted texts. Meanwhile, structured databases for microbiota analysis are available, yet they often lack a comprehensive understanding of the associated biological processes. Therefore, we have devised an approach to construct a comprehensive knowledge graph by combining unstructured textual intelligence with structured database information and applied it to investigate the relationship between pig gut microbes and FE. Firstly, we created the pgmReading knowledge base and the domain ontology of pig gut microbiota by annotating, extracting, and integrating semantic information from 157 scientific publications. Secondly, we created the pgmPubtator by utilizing PubTator to expand the semantic information related to microbiota. Thirdly, we created the pgmDatabase by mapping and combining the ADDAGMA, gutMGene, and KEGG databases based on the ontology. These three knowledge bases were integrated to form the Pig Gut Microbial Knowledge Graph (PGMKG). Additionally, we created five biological query cases to validate the performance of PGMKG. These cases not only allow us to identify microbes with the most significant impact on FE but also provide insights into the metabolites produced by these microbes and the associated metabolic pathways. This study introduces PGMKG, mapping key microbes in pig feed efficiency and guiding microbiota-targeted optimization.

Microbial signatures and enterotype clusters in fattening pigs: implications for nitrogen utilization efficiency

As global demand for pork continues to rise, strategies to enhance nitrogen utilization efficiency (NUE) in pig farming have become vital for environmental sustainability. This study explored the relationship between the fecal microbiota, their metabolites, and NUE in crossbreed fattening pigs with a defined family structure. Pigs were kept under standardized conditions and fed in a two-phase feeding regime. In each phase, one fecal sample was collected from each pig. DNA was extracted from a total of 892 fecal samples and subjected to target amplicon sequencing. The results indicated an influence of sire, sampling period (SP), and sex on the fecal microbiota. Streptococcus emerged as a potential biomarker in comparing high and low NUE pigs in SP 1, suggesting a genetic predisposition to NUE regarding the fecal microbiota. All fecal samples were grouped into two enterotype-like clusters named cluster LACTO and cluster CSST. Pigs' affiliation with enterotype-like clusters altered over time and might be sex-dependent. The stable cluster CSST demonstrated the highest NUE despite containing pigs with lower performance characteristics such as average daily gain, dry matter intake, and daily nitrogen retention. This research contributes with valuable insights into the microbiome's role in NUE, paving the way for future strategies to enhance sustainable pig production.

Citrus Flavonoids Supplementation as an Alternative to Replace Zinc Oxide in Weanling Pigs’ Diets Minimizing the Use of Antibiotics

Since citrus flavonoids have antioxidant and anti-inflammatory properties, it was hypothesized that these compounds would become a suitable alternative to the use of therapeutic doses of zinc oxide at weaning. A total of 252 weaned pigs ([LargeWhite × Landrace] × Pietrain) were distributed according to BW (5.7 kg ± 0.76) into 18 pens (6 pens per diet, 14 pigs/pen). Three experimental diets for the prestarter (0–14 d postweaning) and starter (15–35 d postweaning) period were prepared: (i) a nonmedicated (CON) diet, (ii) a CON diet supplemented with zinc oxide at 2500 mg/kg, amoxicillin at 0.3 mg/kg and apramycin at 0.1 mg/kg (ZnO), and (iii) CON diet with the addition of a commercial citrus flavonoid extract at 0.3 mg/kg and amoxicillin at 0.3 mg/kg (FLAV). Pig BW, ADG, ADFI, and FCR were assessed on d7, d14, and d35, and ADFI and FCR were calculated. Samples of intestinal tissue, cecal content, and serum were collected on day seven (18 piglets). FLAV treatment achieved greater BW and ADG during the starter and for the entire experimental period compared with the CON diet (p < 0.05), whereas ZnO pigs evidenced intermediate results. Jejunum tissue analysis showed that pigs fed the FLAV diet overexpressed genes related to barrier function, digestive enzymes, and nutrient transport compared to those pigs fed the CON diet (p < 0.05). An increase in the abundance of bacterial genera such as Succinivibrio, Turicibacter, and Mitsuokella (p < 0.05) was observed in the FLAV compared with the CON and ZnO piglets. ZnO and FLAV increased the expression of TAS2R39, while ZnO pigs also expressed greater TAS2R16 than CON (p < 0.05) in the intestine. FLAV treatment improved the gut function, possibly explaining a higher performance at the end of the nursery period. Consequently, citrus flavonoids supplementation, together with amoxicillin, is a promising alternative to the use of zinc oxide plus amoxicillin and apramycin in weanling pigs, minimizing the use of antibiotics.

Tributyrin and anise mixture supplementation improves growth performance, nutrient digestibility, jejunal villus height, and fecal microbiota in weaned pigs

Introduction

The objective of this study was to investigate the effects of dietary supplementation of tributyrin and anise mixture (TA) on growth performance, apparent nutrient digestibility, fecal noxious gas emission, fecal score, jejunal villus height, hematology parameters, and fecal microbiota of weaned pigs.

Methods

A total of 150 21-day-old crossbred weaned pigs [(Landrace × Yorkshire) × Duroc] were used in a randomized complete block design experiment. All pigs were randomly assigned to 3 groups based on the initial body weight (6.19 ± 0.29 kg). Each group had 10 replicate pens with 5 pigs (three barrows and two gilts) per pen. The experimental period was 42 days and consisted of 3 phases (phase 1, days 1-7; phase 2, days 8-21; phase 3, days 22-42). Dietary treatments were based on a corn-soybean meal-basal diet and supplemented with 0.000, 0.075, or 0.150% TA.

Results and discussion

We found that dietary supplementation of graded levels of TA linearly improved body weight, body weight gain, average daily feed intake, and feed efficiency (P < 0.05). TA supplementation also had positive effects on apparent dry matter, crude protein, and energy digestibility (P < 0.05) and jejunal villus height (P < 0.05). The emission of ammonia from feces decreased linearly with the dose of TA increased (P < 0.05). Moreover, TA supplementation was capable to regulate the fecal microbiota diversity, manifesting in a linearly increased Chao1 index and observed species and a linearly decreased Pielou's index (P < 0.05). The abundance of Lactobacillus reuteri, Lactobacillus amylovorus, Clostridium butyricum were increased, while the abundance of Prevotella copri was decreased, by treatment (P < 0.05). Therefore, we speculated that TA supplementation would improve growth performance and reduce fecal ammonia emission through improving nutrient digestibility, which was attributed to the increase of jejunal villus height and the regulation of fecal microbiota.

Gut microbiome-produced metabolites in pigs: a review on their biological functions and the influence of probiotics

The gastrointestinal tract is a complex ecosystem that contains a large number of microorganisms with different metabolic capacities. Modulation of the gut microbiome can improve the growth and promote health in pigs. Crosstalk between the host, diet, and the gut microbiome can influence the health of the host, potentially through the production of several metabolites with various functions. Short-chain and branched-chain fatty acids, secondary bile acids, polyamines, indoles, and phenolic compounds are metabolites produced by the gut microbiome. The gut microbiome can also produce neurotransmitters (such as γ-aminobutyric acid, catecholamines, and serotonin), their precursors, and vitamins. Several studies in pigs have demonstrated the importance of the gut microbiome and its metabolites in improving growth performance and feed efficiency, alleviating stress, and providing protection from pathogens. The use of probiotics is one of the strategies employed to target the gut microbiome of pigs. Promising results have been published on the use of probiotics in optimizing pig production. This review focuses on the role of gut microbiome-derived metabolites in the performance of pigs and the effects of probiotics on altering the levels of these metabolites.

Different dietary starch patterns in low-protein diets: effect on nitrogen efficiency, nutrient metabolism, and intestinal flora in growing pigs

Background

Protein releases amino acids faster than starch releases glucose in digestive tract of pigs fed low-protein (LP) diets. Poor synchronization of dietary glucose and amino acids supply leads to compromised nitrogen efficiency. Dietary starch patterns modulation may improve this situation.

Methods

Growing barrows (29.7 ± 2.0 kg) were randomly allotted into 5 dietary treatments with LP diets consisting of different purified starches. Treatments included: waxy corn starch (W LP), corn starch + waxy corn starch (C + W LP), corn starch (C LP), pea starch + waxy corn starch (P + W LP) and pea starch (P LP). In the experiment, growth performance, protein deposition, nutrient metabolism, and fecal microbial community of pigs were investigated. In vitro starch digestion was used for predicting the in vivo glucose response.

Results

Dietary starch in vitro glucose release profile was determined by starch source and the ratio of amylopectin and amylose. C + W LP treatment showed decreased total nitrogen excretion and plasma citrulline concentration and improved plasma leptin concentration among treatments (P < 0.05). Besides, the highest nitrogen apparent biological value, whole-body protein deposition and growth performance and lowest urinary nitrogen excretion were also observed in C + W LP treatment. Compared with the other groups, C + W LP and C LP showed increased plasma pyruvate, IGF-1, and lipase concentrations (P < 0.05). The W LP group presented dramatically increased plasma alanine and urea nitrogen concentration and decreased aldolase and leptin concentrations (P < 0.05). Dietary starch patterns did not make an impact on bacterial richness and diversity, but changed the taxonomic and functional structures of the microbial communities. Microbial protein fermentation product (isobutyrate and isovalerate) presented increased in P LP treatments compared with the other treatments (P < 0.05).

Conclusions

Dietary starch patterns modulation can regulate dietary glucose release profile, nutrient metabolism, protein turnover, and fecal microbial fermentation in pigs. The optimal dietary glucose release profile effectively strengthened whole-body protein deposition and improve nitrogen efficiency and growth performance in growing pigs fed LP diets.

Temporal and nutritional effects on the weaner pig ileal microbiota

BACKGROUND

The porcine gastrointestinal microbiota has been linked to both host health and performance. Most pig gut microbiota studies target faecal material, which is not representative of microbiota dynamics in other discrete gut sections. The weaning transition period in pigs is a key development stage, with gastrointestinal problems being prominent after often sudden introduction to a solid diet. A better understanding of both temporal and nutritional effects on the small intestinal microbiota is required. Here, the development of the porcine ileal microbiota under differing levels of dietary protein was observed over the immediate post-weaning period.

RESULTS

Ileal digesta samples were obtained at post-mortem prior to weaning day (day - 1) for baseline measurements. The remaining pigs were introduced to either an 18% (low) or 23% (high) protein diet on weaning day (day 0) and further ileal digesta sampling was carried out at days 5, 9 and 13 post-weaning. We identified significant changes in microbiome structure (P = 0.01), a reduction in microbiome richness (P = 0.02) and changes in the abundance of specific bacterial taxa from baseline until 13 days post-weaning. The ileal microbiota became less stable after the introduction to a solid diet at weaning (P = 0.036), was highly variable between pigs and no relationship was observed between average daily weight gain and microbiota composition. The ileal microbiota was less stable in pigs fed the high protein diet (P = 0.05), with several pathogenic bacterial genera being significantly higher in abundance in this group. Samples from the low protein and high protein groups did not cluster separately by their CAZyme (carbohydrate-active enzyme) composition, but GH33 exosialidases were found to be significantly more abundant in the HP group (P = 0.006).

CONCLUSIONS

The weaner pig ileal microbiota changed rapidly and was initially destabilised by the sudden introduction to feed. Nutritional composition influenced ileal microbiota development, with the high protein diet being associated with an increased abundance of significant porcine pathogens and the upregulation of GH33 exosialidases-which can influence host-microbe interactions and pathogenicity. These findings contribute to our understanding of a lesser studied gut compartment that is not only a key site of digestion, but also a target for the development of nutritional interventions to improve gut health and host growth performance during the critical weaning transition period.

Variations in Microbial Diversity and Metabolite Profiles of Female Landrace Finishing Pigs With Distinct Feed Efficiency

To enhance pig production, feed efficiency (FE) should be improved; however, the mechanisms by which gut microbes affect FE in pigs have not been fully elucidated. To investigate the differences between the composition and functionality of the gut microbiota associated with low and high FE, microbial compositions were characterized using 16S rRNA sequencing, functional annotations were performed by shotgun metagenomics, and metabolomic profiles were created by GC-TOF-MS from female Landrace finishing pigs with low and high feed conversion ratios (FCRs). Lactobacillus was enriched in the gut microbiota of individuals with low FCRs (and thus high FE), while Prevotella abundance was significantly higher in individuals with high FCRs (and thus low FE). This may be linked to carbohydrate consumption and incomplete digestion. The activity of pathways involved in the metabolism of cofactors and vitamins was greater in pigs with lower FE. We also identified differences in pyruvate-related metabolism, including phenylalanine and lysine metabolism. This suggests that pyruvate metabolism is closely related to microbial fermentation in the colon, which in turn affects glycolysis. This study deepens our understanding of how gut microbiota are related to pig growth traits, and how regulating microbial composition could aid in improving porcine FE. However, these results need to be validated using a larger pig cohort in the future.

Impact of Intestinal Microbiota on Growth and Feed Efficiency in Pigs: A Review

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

Selection of Immunobiotic Ligilactobacillus salivarius Strains from the Intestinal Tract of Wakame-Fed Pigs: Functional and Genomic Studies

In this article, Ligilactobacillus salivarius FFIG strains, isolated from the intestinal tract of wakame-fed pigs, are characterized according to their potential probiotic properties. Strains were evaluated by studying their interaction with porcine intestinal epithelial (PIE) cells in terms of their ability to regulate toll-like receptor (TLR)-3- or TLR4-mediated innate immune responses, as well as by assessing their adhesion capabilities to porcine epithelial cells and mucins. These functional studies were complemented with comparative genomic evaluations using the complete genome sequences of porcine L. salivarius strains selected from subgroups that demonstrated different “immune” and “adhesion” phenotypes. We found that their immunomodulatory and adhesion capabilities are a strain-dependent characteristic. Our analysis indicated that the differential immunomodulatory and adhesive activities of FFIG strains would be dependent on the combination of several surface structures acting simultaneously, which include peptidoglycan, exopolysaccharides, lipoteichoic acid, and adhesins. Of note, our results indicate that there is no correlation between the immunomodulatory capacity of the strains with their adhesion ability to mucins and epithelial cells. Therefore, in the selection of strains destined to colonize the intestinal mucosa and modulate the immunity of the host, both properties must be adequately evaluated. Interestingly, we showed that L. salivarius FFIG58 functionally modulated the innate immune responses triggered by TLR3 and TLR4 activation in PIE cells and efficiently adhered to these cells. Moreover, the FFIG58 strain was capable of reducing rotavirus replication in PIE cells. Therefore, L. salivarius FFIG58 is a good candidate for further in vivo studying the protective effect of lactobacilli against intestinal infections in the porcine host. We also reported and analyzed, for the first time, the complete genome of several L. salivarius strains that were isolated from the intestine of pigs after the selective pressure of feeding the animals with wakame. Further genomic analysis could be of value to reveal the metabolic characteristics and potential of the FFIG strains in general and of the FFIG58 strain, in particular, relating to wakame by-products assimilation.

Evaluation of Bacillus licheniformis-Fermented Feed Additive as an Antibiotic Substitute: Effect on the Growth Performance, Diarrhea Incidence, and Cecal Microbiota in Weaning Piglets

This study investigated the potential of a Bacillus licheniformis-fermented feed additive (BLF) as an antibiotic substitute in weaning piglets. Ninety-six crossbred piglets were randomly allotted into four treatments with three replicate pens per treatment and eight pigs per pen. Piglets were fed diets as follows: a basal diet as control, a basal diet supplemented with bacitracin (30 mg/kg of bacitracin methylene disalicylate), a basal diet supplemented with BLF (1 g/kg of the Bacillus licheniformis-fermented feed additive), and a basal diet supplemented with bacitracin and BLF (15 mg/kg of bacitracin methylene disalicylate and 0.5 g/kg of the Bacillus licheniformis-fermented feed additive). The results showed that replacing all or half the bacitracin with BLF both reduced the incidence of diarrhea in weaning piglets from day 1 to 14. Principal coordinates analysis and a species abundance heat map showed that distinct clusters were formed between groups. Replacing all the bacitracin with BLF reduced bacterial evenness in the cecal digesta of weaning piglets, while the inhibitory effect on bacterial evenness was reversed in the group treated with bacitracin in combination with BLF. These results indicated that the half replacement of bacitracin with BLF was able to decrease the incidence of diarrhea and modify cecal microbiota composition in weaning piglets, suggesting that a Bacillus licheniformis-fermented feed additive has good potential as a suitable alternative to antibiotics use in the swine industry.

Combined Use of Bacillus subtilis yb-114,246 and Bacillus licheniformis yb-214,245 Improves Body Growth Performance of Chinese Huainan Partridge Shank Chickens by Enhancing Intestinal Digestive Profiles

The aim of our study was to unveil the promoting function of compound Bacillus sp. in improving chicken digestion-induced higher body growth performance. Strains of Bacillus subtilis and B. licheniformis were jointly supplemented to the chick diet. Digestive enzyme activities in the digesta improved, development of intestinal villus enhanced, and duodenum and ileum villous height increased, while their crypt depth declined, and the cecum's bacterial composition optimized after 56 days of supplementation. Bacterial composition at the phylum level changed significantly, more Firmicutes, Proteobacteria, Epsilonbacteraeota, and Tenericutes, but fewer Bacteroidetes were detected in cecum digesta in the compound Bacillus supplemented group. Bacterial composition diversity, which improves the abundances of metabolic genes through KEGG pathway classification, became more abundant. Results indicated that the Ruminococcaceae UCG-005, unclassified Ruminococcaceae, and unclassified Lachnospiraceae species are actively correlated with body growth, promoting higher final body weight. In conclusion, owing to digestive enzyme secretion, the development of intestinal villus was stimulated and gastrointestinal bacterial composition optimized, and two combined Bacillus sp. improved chicken body growth. Our findings show the promoting action of Bacillus subtilis and B. licheniformis on digestion, which can be an alternative to antibiotics.