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

Exploring the Effect of Gastrointestinal Prevotella on Growth Performance Traits in Livestock Animals

Microorganisms in the rumen play a crucial role in determining the most efficient utilization rate of nutrients. Among these microorganisms, Prevotella stands out as one of the most representative bacteria within the rumen biological system. Prevotella is a common strict anaerobic bacterium that is found in the gastrointestinal tract of livestock. Prevotella plays a crucial role in breaking down and metabolizing complex nutrients like cellulose and protein during food digestion. Moreover, it is capable of working together with other bacteria in the body's digestive system. Several studies have shown a strong correlation between the abundance of Prevotella and livestock growth performance. This paper provides a comprehensive review of the current research on the function, mechanisms, and applications of Prevotella in the gastrointestinal tract. The insights provided in this review could serve as a theoretical basis for accurately classifying Prevotella, further investigating its effects and potential mechanisms on livestock growth performance, and exploring its practical applications.

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.

Colonic Microbiota Improves Fiber Digestion Ability and Enhances Absorption of Short-Chain Fatty Acids in Local Pigs of Hainan

Compared to commercial breeds, Chinese local pig breeds have a greater ability to digest dietary fiber, which may be due to differences in intestinal microbiota. In this study, we fed Ding'an and DLY pigs high and low levels of dietary fiber, respectively, to investigate factors contributing to high dietary fiber adaption in Ding'an pigs. Twelve Ding'an pigs and DLY pigs were randomly divided into a 2 (diet) × 2 (breed) factorial experiment (n = 3). Compared with commercial pigs, Ding'an pigs have a stronger ability to digest dietary fiber. Prevotella was more prevalent in Ding'an pigs than in DLY pigs, which may be an important reason for the stronger ability of fiber degradation in Ding'an pigs. When the effects of feed and breed factors are considered, differences in abundance of 31 species and 14 species, respectively, may result in a greater ability of fiber degradation in Ding'an pigs. Among them, Prevotella. sp. CAG:520 may be a newly discovered bacterium related to fiber degradation, which positively correlated with many fiber-degrading bacteria (r > 0.7). We also found that the concentration of plant metabolites with anti-inflammatory and antioxidant effects was higher in the colonic chyme of Ding'an pigs after increasing the fiber content, which resulted in the downregulated expression of inflammatory factors in colonic mucosa. Spearman's correlation coefficient revealed a strong correlation between microbiota and the apparent digestibility of dietary fiber (r > 0.7). The mRNA expressions of SLC16A1, PYY, and GCG were significantly increased in the colonic mucosa of Ding'an pigs fed on high-fiber diets, which indicates that Ding'an pigs have an enhanced absorption of SCFAs. Our results suggested that an appropriate increase in dietary fiber content can reduce the inflammatory response and improve feed efficiency in Ding'an pigs, and differences in the intestinal microbial composition may be an important reason for the difference in the fiber degradation capacity between the two breeds of pigs.

Relationship between feed efficiency and gut microbiota in laying chickens under contrasting feeding conditions

The gut microbiota is known to play an important role in energy harvest and is likely to affect feed efficiency. In this study, we used 16S metabarcoding sequencing to analyse the caecal microbiota of laying hens from feed-efficient and non-efficient lines obtained by divergent selection for residual feed intake. The two lines were fed either a commercial wheat-soybean based diet (CTR) or a low-energy, high-fibre corn-sunflower diet (LE). The analysis revealed a significant line x diet interaction, highlighting distinct differences in microbial community composition between the two lines when hens were fed the CTR diet, and more muted differences when hens were fed the LE diet. Our results are consistent with the hypothesis that a richer and more diverse microbiota may play a role in enhancing feed efficiency, albeit in a diet-dependent manner. The taxonomic differences observed in the microbial composition seem to correlate with alterations in starch and fibre digestion as well as in the production of short-chain fatty acids. As a result, we hypothesise that efficient hens are able to optimise nutrient absorption through the activity of fibrolytic bacteria such as Alistipes or Anaerosporobacter, which, via their production of propionate, influence various aspects of host metabolism.

Enhancing Weaned Piglet Health and Performance: The Role of Autolyzed Yeast (Saccharomyces cerevisiae) and β-Glucans as a Blood Plasma Alternative in Diets

The objective of this study was to evaluate the inclusion of the autolyzed yeast (AY) Saccharomyces cerevisiae with or without an immunomodulator (1,3/1,6 β-glucans) as a total/partial substitute for blood plasma (BP) in the diet of post-weaning piglets; zootechnical performance, intestinal health and microbiota, immune responses and energy metabolism were assessed. A total of 240 castrated male and female piglets, with a mean age of 22 days and mean initial weight of 5.24 ± 0.82 kg, were randomly divided into blocks of four treatments with 12 replicates. The dietary inclusions were blood plasma (BP), autolyzed yeast (AY), autolyzed yeast + immunomodulator (AYI) and 50% BP and 50% AY (BPAY). In pre-initial phase II (29-35 days), piglets fed AY showed better feed conversion (FCR = 1.358) than the piglets in the BP (1.484), AYI (1.379) and BPAY (1.442) groups, i.e., 8.49% (0.126), 1.52% (0.021) and 4.50% (0.084), respectively (p = 0.0293). In the total period (21-42 days), better FCR was observed in the AYI (1.458) group, i.e., 4.64% (0.071), 1.15% (0.017) and 4.58% (0.070), than in the BP (1.529), AY (1.475) and BPAY (1.528) groups, respectively (p = 0.0150). In piglets fed AY (n = 3) and BPAY (n = 2), there was a reduction in the number of medications, i.e., 82.35% (-14n) and 88.23% (-15n), respectively (p = 0.0001), compared with that in the BP group (n = 17). In the AY group (73.83 mg/dL), AYI group (69.92 mg/dL), and BPAY group (69.58 mg/dL), piglets exhibited increases in triglyceride levels of 79.32%, 69.83%, and 69.00%, respectively, in comparison to those in the BP group, which had triglyceride levels of 41.17 mg/dL (p = 0.0400). The beta-hydroxybutyrate concentration in the AY group (79.96 ng/μL) was lower by 31.95%, 22.64%, and 5.89% compared to the BP group (117.50 ng/μL), AYI group (103.36 ng/μL), and BPAY group (84.67 ng/μL), respectively (p = 0.0072). In the AYI group, there was modulation of the microbiota, with an increase in the relative abundance of bacteria of the genera Lactobacillus, Collinsella and Bulleidia. AY, associated or not associated with an immunomodulator, is a potential substitute for BP in diets for piglets in the nursery phase, with positive effects on immune, metabolic, and intestinal microbial performance.

Swine Gastrointestinal Microbiota and the Effects of Dietary Amino Acids on Its Composition and Metabolism

Many researchers consider gut microbiota (trillions of microorganisms) an endogenous organ of its animal host, which confers a vast genetic diversity in providing the host with essential biological functions. Particularly, the gut microbiota regulates not only gut tissue structure but also gut health and gut functionality. This paper first summarized those common bacterial species (dominated by the Firmicutes, Bacteroidota, and Proteobacteria phyla) in swine gut and then briefly discussed their roles in swine nutrition and health, which include roles in nutrient metabolism, pathogen exclusion, and immunity modulation. Secondly, the current knowledge on how dietary nutrients and feed additives affect the gut bacterial composition and nutrient metabolism in pigs was discussed. Finally, how dietary amino acids affect the relative abundances and metabolism of bacteria in the swine gut was reviewed. Tryptophan supplementation promotes the growth of beneficial bacteria and suppresses pathogens, while arginine metabolism affects nitrogen recycling, impacting gut immune response and health. Glutamate and glutamine supplementations elevate the levels of beneficial bacteria and mitigate pathogenic ones. It was concluded that nutritional strategies to manipulate gut microbial ecosystems are useful measures to optimize gut health and gut functions. For example, providing pigs with nutrients that promote the growth of Lactobacillus and Bifidobacterium can lead to better gut health and growth performance, especially when dietary protein is limited. Further research to establish the mechanistic cause-and-effect relationships between amino acids and the dynamics of gut microbiota will allow swine producers to reap the greatest return on their feed investment.

Characterizing core microbiota and regulatory functions of the pig gut microbiome

Domestic pigs (Sus scrofa) are the leading terrestrial animals used for meat production. The gut microbiota significantly affect host nutrition, metabolism, and immunity. Hence, characterization of the gut microbial structure and function will improve our understanding of gut microbial resources and the mechanisms underlying host-microbe interactions. Here, we investigated the gut microbiomes of seven pig breeds using metagenomics and 16S rRNA gene amplicon sequencing. We established an expanded gut microbial reference catalog comprising 17 020 160 genes and identified 4910 metagenome-assembled genomes. We also analyzed the gut resistome to provide an overview of the profiles of the antimicrobial resistance genes in pigs. By analyzing the relative abundances of microbes, we identified three core-predominant gut microbes (Phascolarctobacterium succinatutens, Prevotella copri, and Oscillibacter valericigenes) in pigs used in this study. Oral administration of the three core-predominant gut microbes significantly increased the organ indexes (including the heart, spleen, and thymus), but decreased the gastrointestinal lengths in germ-free mice. The three core microbes significantly enhanced intestinal epithelial barrier function and altered the intestinal mucosal morphology, as was evident from the increase in crypt depths in the duodenum and ileum. Furthermore, the three core microbes significantly affected several metabolic pathways (such as "steroid hormone biosynthesis," "primary bile acid biosynthesis," "phenylalanine, tyrosine and tryptophan biosynthesis," and "phenylalanine metabolism") in germ-free mice. These findings provide a panoramic view of the pig gut microbiome and insights into the functional contributions of the core-predominant gut microbes to the host.

Genetic association and bidirectional Mendelian randomization for causality between gut microbiota and six lung diseases

Purposes

Increasing evidence suggests that intestinal microbiota correlates with the pathological processes of many lung diseases. This study aimed to investigate the causality of gut microbiota and lung diseases.

Methods

Genetic information on intestinal flora and lung diseases [asthma, chronic bronchitis, chronic obstructive pulmonary disease (COPD), interstitial lung disease (ILD), lower respiratory tract infection (LRTI), pulmonary arterial hypertension (PAH)] and lung function was obtained from UK Biobank, FinnGen, and additional studies. A Mendelian randomization (MR) analysis was conducted to explore the causal association between gut microbiota and lung diseases.

Results

The genetic liability to lung diseases may be associated with the abundance of certain microbiota taxa. Specifically, the genus Prevotella (p = 0.041) was related to a higher risk of asthma; the family Defluviitaleaceae (p = 0.002) and its child taxon were identified as a risk factor for chronic bronchitis; the abundance of the genus Prevotella (p = 0.020) was related to a higher risk of ILD; the family Coriobacteriaceae (p = 0.011) was identified to have a positive effect on the risk of LRTI; the genus Lactobacillus (p = 0.0297) has been identified to be associated with an increased risk of PAH, whereas the genus Holdemanella (p = 0.0154) presented a causal decrease in COPD risk; the order Selenomonadales was identified to have a positive effect on the risk of FEV1(p = 0.011). The reverse TSMR analysis also provided genetic evidence of reverse causality from lung diseases to the gut microbiota.

Conclusion

This data-driven MR analysis revealed that gut microbiota was causally associated with lung diseases, providing genetic evidence for further mechanistic and clinical studies to understand the crosstalk between gut microbiota and lung diseases.

Assessing the Probiotic Effects of Pediococcus pentosaceus CACC616 in Weaned Piglets

During weaning, piglets experience various stressor events that disrupt their gut microbiota and immune balance, decrease growth parameters, and increase mortality rates. In this study, we assessed the efficacy of Pediococcus pentosaceus CACC616 as a probiotic supplement. We characterized this strain and evaluated its effect on improving growth performance, modulating gut microbiota composition, and reducing noxious odor components in weaned piglets compared to a non-supplementary diet (control). During the 26-day period, 40 crossbred weaned piglets were randomly assigned to pens with 20 animals each in two groups: control and treatment groups with CACC616. On day 26, the treatment group exhibited a lower feed conversion ratio (FCR) and a significant alteration in gut microbial composition, correlating with improved growth parameters and gut health (p < 0.05). The treatment group also exhibited significantly reduced digestibility- and intestinal-environment-related noxious odor components (p < 0.05). The CACC616 strain effectively reduced pathogenic genera numbers, including Campylobacter, Mogibacterium, Escherichia-Shigella, and Desulfovibrio spp., with the treatment group exhibiting lower fecal calprotectin levels than the control group (p < 0.05). Overall, this study revealed that the functional probiotic CACC616 contributes to enhanced FCR and effectively modulates weaned piglets' inflammation and intestinal microbiota.

Modulation of Swine Gut Microbiota by Phytogenic Blends and High Concentrations of Casein in a Validated Swine Large Intestinal In Vitro Model

Phytogenic feed additives are gaining popularity in livestock as a replacement for antibiotic growth promotors. Some phytogenic blends (PB) positively affect the production performance, inhibit pathogens within the gut microbiota, and improve the overall health of farm animals. In this study, a swine large intestine in vitro model was used to evaluate the effect of two PBs, alone or in combination with casein, on swine gut microbiota. As a result, the combination of casein with PB1 had the most beneficial effects on swine gut microbiota, as it increased the relative abundance of some commensal bacteria and two genera (Lactobacillus and Oscillospiraceae UCG-002), which are associated with greater production performance in pigs. At the same time, supplementation with PBs did not lead to an increase in opportunistic pathogens, indicating their safety for pigs. Both PBs showed fewer changes in swine gut microbiota compared to interventions with added casein. In contrast, casein supplementation significantly increased beta diversity and the relative abundance of commensal as well as potentially beneficial bacteria. In conclusion, the combination of casein with PBs, in particular PB1, had the most beneficial effects among the studied supplements in vitro, with respect to microbiota modulation and metabolite production, although this data should be proven in further in vivo studies.

Influence of Sex and a High-Fiber Diet on the Gut Microbiome of Alentejano Pigs Raised to Heavy Weights

This study investigates the influence of sex and a dietary transition on the gut microbiota of a local Portuguese pig breed. Three groups of male Alentejano pigs (n = 10 each) were raised between ~40 and 160 kg LW. Group C included pigs that were surgically castrated, while the I group included intact ones; both were fed with commercial diets. The third group, IExp, included intact pigs that were fed commercial diets until ~130 kg, then replaced by an experimental diet based on legumes and agro-industrial by-products between ~130 and 160 kg. Fecal samples were collected two weeks before slaughter. The total DNA was extracted and used for 16S metabarcoding on a MiSeq® System. The dietary transition from a commercial diet to the experimental diet substantially increased and shifted the diversity observed. Complex carbohydrate fermenting bacteria, such as Ruminococcus spp. and Sphaerochaeta spp., were significantly more abundant in IExp (q < 0.05). On the other hand, castrated pigs presented a significantly lower abundance of the potential probiotic, Roseburia spp. and Lachnospiraceae NK4A136 group (q < 0.01), bacteria commonly associated with better gut health and lower body fat composition. Understanding the role of gut microbiota is paramount to ensure a low skatole deposition and consumers' acceptance of pork products from non-castrated male pigs.

When digestive physiology doesn't match "diet": Lumpenus sagitta (Stichaeidae) is an "omnivore" with a carnivorous gut

What an animal ingests and what it digests can be different. Thus, we examined the nutritional physiology of Lumpenus sagitta, a member of the family Stichaeidae, to better understand whether it could digest algal components like its better studied algivorous relatives. Although L. sagitta ingests considerable algal content, we found little evidence of algal digestion. This fish species has a short gut that doesn't show positive allometry with body size, low amylolytic activity that actually decreases as the fish grow, no ontogenetic changes in digestive enzyme gene expression, elevated N-acetyl-glucosaminidase activity (indicative of chitin breakdown), and an enteric microbial community that is consistent with carnivory and differs from members of its family that consume and digest algae. Hence, we are left concluding that L. sagitta is not capable of digesting the algae it consumes, and instead, are likely targeting epibionts on the algae itself, and other invertebrates consumed with the algae. Our study expands the coverage of dietary and digestive information for the family Stichaeidae, which is becoming a model for fish digestive physiology and genomics, and shows the power of moving beyond gut content analyses to better understand what an animal can actually digest and use metabolically.

A Comparative Study on the Growth Performance and Gut Microbial Composition of Duroc and Yorkshire Boars

The intestinal microbiota is required for maintaining the development and health of the host. However, the gut microbiota contributing to the regulation of the growth performance and health of Duroc and Yorkshire boars remains largely unknown. In this study, we first evaluated the difference in the growth performance between Duroc and Yorkshire boars when their body weight reached 100 kg. Relative to Duroc boars, Yorkshire boars weighed 100 kg at a younger age and exhibited a significantly lower backfat thickness and eye muscle area. Microbial analysis of the fecal samples revealed a marked difference in gut microbiota composition between the two pig models and remarkably increased α-diversity in Yorkshire boars compared to Duroc boars. Further analysis indicated that Bacteroidota, Prevotellaceae, and Ruminococcaceae might be associated with the growth performance and lean meat rate of Yorkshire boars. Taken together, these results highlight that Yorkshire boars exhibit a faster growth rate and higher lean meat rate compared to Duroc boars, and these differences may be attributed to the influence of the gut microbiota, thereby providing valuable insight into optimizing pig breeding systems and selecting terminal paternal sires to enhance overall productivity and quality.

Swine gut microbiome associated with non-digestible carbohydrate utilization

Non-digestible carbohydrates are an unavoidable component in a pig's diet, as all plant-based feeds contain different kinds of non-digestible carbohydrates. The major types of non-digestible carbohydrates include non-starch polysaccharides (such as cellulose, pectin, and hemicellulose), resistant starch, and non-digestible oligosaccharides (such as fructo-oligosaccharide and xylo-oligosaccharide). Non-digestible carbohydrates play a significant role in balancing the gut microbial ecology and overall health of the swine by promoting the production of short chain fatty acids. Although non-digestible carbohydrates are rich in energy, swine cannot extract this energy on their own due to the absence of enzymes required for their degradation. Instead, they rely on gut microbes to utilize these carbohydrates for energy production. Despite the importance of non-digestible carbohydrate degradation, limited studies have been conducted on the swine gut microbes involved in this process. While next-generation high-throughput sequencing has aided in understanding the microbial compositions of the swine gut, specific information regarding the bacteria involved in non-digestible carbohydrate degradation remains limited. Therefore, it is crucial to investigate and comprehend the bacteria responsible for the breakdown of non-digestible carbohydrates in the gut. In this mini review, we have discussed the major bacteria involved in the fermentation of different types of non-digestible carbohydrates in the large intestine of swine, shedding light on their potential roles and contributions to swine nutrition and health.

Comparison of the Faecal Microbiota Composition Following a Dairy By-Product Supplemented Diet in Nero Siciliano and Large White × Landrace Pig Breeds

The current study compared the faecal microbiota composition of two pig breeds (autochthonous vs. commercial) to understand what happens after the integration of liquid whey in the diet and what the role of the host genetic is. The trial was conducted for 60 days, and the faecal microbiota composition was investigated at three time points, T0, T1 (after 30 days) and T2 (after 60 days) in 30 female pigs (20 commercial crossbred and 10 Nero Siciliano pigs). The animals were divided into four groups (two control and two treatment groups). Generally, in both breeds, Firmicutes (51%) and Bacteroidota (36%) were the most abundant phylum whereas Prevotella, Treponema and Lactobacillus were the most abundant genera. The two breeds have a different reaction to a liquid whey diet. In fact, as shown by PERMANOVA analysis, the liquid whey significantly (p < 0.001) affects the microbiota composition of crossbreeds while not having an effect on the microbiota of the Nero Siciliano. Despite this, in both breeds Bifidobacterium and Ruminococcus have been positively influenced by liquid whey and they promote intestinal health, improve immunity, increase performance, and feed efficiency. In conclusion, the integration of liquid whey had a different effect on the Nero Siciliano and crossbred pig breeds, emphasizing the importance of the host genetic profile in determining the faecal bacterial composition.

Impact of Intestinal Microbiota on Growth Performance of Suckling and Weaned Piglets

Small-scale studies investigating the relationship between pigs' intestinal microbiota and growth performance have generated inconsistent results. We hypothesized that on farms under favorable environmental conditions (e.g., promoting sow nest-building behavior, high colostrum production, low incidence of diseases and minimal use of antimicrobials), the piglet gut microbiota may develop toward a population that promotes growth and reduces pathogenic bacteria. Using 16S rRNA gene amplicon sequencing, we sampled and profiled the fecal microbiota from 170 individual piglets throughout suckling and postweaning periods (in total 670 samples) to track gut microbiota development and its potential association with growth. During the suckling period, the dominant genera were Lactobacillus and Bacteroides, the latter being gradually replaced by Clostridium sensu scricto 1 as piglets aged. The gut microbiota during the nursery stage, not the suckling period, predicted the average daily growth (ADG) of piglets. The relative abundances of SCFA-producing genera, in particular Faecalibacterium, Megasphaera, Mitsuokella, and Subdoligranulum, significantly correlated with high ADG of weaned piglets. In addition, the succession of the gut microbiota in high-ADG piglets occurred faster and stabilized sooner upon weaning, whereas the gut microbiota of low-ADG piglets continued to mature after weaning. Overall, our findings suggest that weaning is the major driver of gut microbiota variation in piglets with different levels of overall growth performance. This calls for further research to verify if promotion of specific gut microbiota, identified here at weaning transition, is beneficial for piglet growth. IMPORTANCE The relationship between pigs' intestinal microbiota and growth performance is of great importance for improving piglets' health and reducing antimicrobial use. We found that gut microbiota variation is significantly associated with growth during weaning and the early nursery period. Importantly, transitions toward a mature gut microbiota enriched with fiber-degrading bacteria mostly complete upon weaning in piglets with better growth. Postponing the weaning age may therefore favor the development of fiber degrading gut bacteria, conferring the necessary capacity to digest and harvest solid postweaning feed. The bacterial taxa associated with piglet growth identified herein hold potential to improve piglet growth and health.

Dietary Probiotics Modulate Gut Barrier and Immune-Related Gene Expression and Histomorphology in Broiler Chickens under Non- and Pathogen-Challenged Conditions: A Meta-Analysis

Data published in the literature about the favorable effects of dietary probiotics on gut health in broiler chickens are inconsistent. To obtain a more comprehensive understanding, we conducted a meta-analysis to assess the effects of probiotics on the gut barrier and immune-related gene expression, histomorphology, and growth in chickens that were either challenged or non-challenged with pathogens. From the 54 articles published between 2012 and 2022, subsets of data, separately for non-challenged and challenged conditions, for response variables were created. The mean dietary probiotic concentrations ranged from 4.7 to 6.2 and 4.7 to 7.2 log₁₀ colony-forming unit/kg under non-challenged and challenged conditions, respectively. Probiotics increased the expression of genes for mucins and tight junction proteins in the jejunum and ileum at weeks 3 and 6. The stimulatory effect of probiotics on tight junction protein expression was partly stronger in challenged than in non-challenged birds. Meta-regressions also showed an anti-inflammatory effect of probiotics under challenged conditions by modulating the expression of cytokines. Probiotics improved villus height at certain ages in the small intestine while not influencing growth performance. Dietary metabolizable energy, crude protein, and days post-infection modified the effects of probiotics on the observed variables. Overall, meta-regressions support the beneficial effects of probiotics on gut integrity and structure in chickens.

Maternal and/or post-weaning supplementation with Bacillus altitudinis spores modulates the microbial composition of colostrum, digesta and faeces in pigs

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

Effects of Major Families of Modulators on Performances and Gastrointestinal Microbiota of Poultry, Pigs and Ruminants: A Systematic Approach

Considering the ban on the use of antibiotics as growth stimulators in the livestock industry, the use of microbiota modulators appears to be an alternative solution to improve animal performance. This review aims to describe the effect of different families of modulators on the gastrointestinal microbiota of poultry, pigs and ruminants and their consequences on host physiology. To this end, 65, 32 and 4 controlled trials or systematic reviews were selected from PubMed for poultry, pigs and ruminants, respectively. Microorganisms and their derivatives were the most studied modulator family in poultry, while in pigs, the micronutrient family was the most investigated. With only four controlled trials selected for ruminants, it was difficult to conclude on the modulators of interest for this species. For some modulators, most studies showed a beneficial effect on both the phenotype and the microbiota. This was the case for probiotics and plants in poultry and minerals and probiotics in pigs. These modulators seem to be a good way for improving animal performance.

Identification of gut microbes associated with feed efficiency by daily-phase feeding strategy in growing-finishing pigs

Feed efficiency is one of the most important issues for sustainable pig production. Daily-phase feeding (DPF) is a form of precision feeding that could improve feed efficiency in pigs. Gut microbiota can regulate host nutrient digestion, absorption, and metabolism. However, which key microbes may play a vital role in improving the feed efficiency during DPF remains unclear. In the present study, we used a DPF program compared to a three-phase feeding (TPF) program in growing-finishing pigs to investigate the effects of gut microbiota on feed efficiency. A total of 204 Landrace × Yorkshire pigs (75 d) were randomly assigned into 2 treatments. Each treatment was replicated 8 times with 13 to 15 pigs per replicate pen. Pigs in the TPF group were fed with a commercial feeding program that supplied fixed feed for phases I, II, and III, starting at 81, 101, and 132 d of age, respectively, and pigs in the DPF group were fed a blend of adjacent phase feed from 81 to 155 d at a gradual daily ratio and phase III feed from 155 to 180 d of age. Daily feed intake and body weight were recorded by a computerized device in the feeders. Feces and blood samples were collected from 1 pig per replicate at 155 and 180 d of age. The results showed that the DPF program remarkably improved the feed efficiency at 155 d (P < 0.001) and 180 d of age (P < 0.001), with a significant reduction of the intake of crude protein (P < 0.01), net energy (P < 0.001), crude fiber (P < 0.001), ether extract (P < 0.01), and ash (P < 0.001). The daily-phase feeding program increased the abundance of Prevotella copri (P < 0.05) and Paraprevotella clara (P < 0.05), while it decreased the abundance of Ocilibacter (P < 0.05) at 155 d of age. The results of correlation analysis indicated that the differentially abundant microbiota communities were closely associated with 20 metabolites which enriched amino acid and phenylalanine metabolism. Our results suggest that 2 key microbes may contribute to feed efficiency during daily-phase feeding strategies in pigs.

Reprogramming of the gut microbiota following feralization in Sus scrofa

BACKGROUND

Wild boar has experienced several evolutionary trajectories from which domestic (under artificial selection) and the feral pig (under natural selection) originated. Strong adaptation deeply affects feral population's morphology and physiology, including the microbiota community. The gut microbiota is generally recognized to play a crucial role in maintaining host health and metabolism. To date, it is unclear whether feral populations' phylogeny, development stages or lifestyle have the greatest impact in shaping the gut microbiota, as well as how this can confer adaptability to new environments. Here, in order to deepen this point, we characterized the gut microbiota of feral population discriminating between juvenile and adult samples, and we compared it to the microbiota structure of wild boar and domestic pig as the references. Gut microbiota composition was estimated through the sequencing of the partial 16S rRNA gene by DNA metabarcoding and High Throughput Sequencing on DNA extracted from fecal samples.

RESULTS

The comparison of microbiota communities among the three forms showed significant differences. The feral form seems to carry some bacteria of both domestic pigs, derived from its ancestral condition, and wild boars, probably as a sign of a recent re-adaptation strategy to the natural environment. In addition, interestingly, feral pigs show some exclusive bacterial taxa, also suggesting an innovative nature of the evolutionary trajectories and an ecological segregation in feral populations, as already observed for other traits.

CONCLUSIONS

The feral pig showed a significant change between juvenile and adult microbiota suggesting an influence of the wild environment in which these populations segregate. However, it is important to underline that we certainly cannot overlook that these variations in the structure of the microbiota also depended on the different development stages of the animal, which in fact influence the composition of the intestinal microbiota. Concluding, the feral pigs represent a new actor living in the same geographical space as the wild boars, in which its gut microbial structure suggests that it is mainly the result of environmental segregation, most different from its closest relative. This gives rise to interesting fields of exploration regarding the changed ecological complexity and the consequent evolutionary destiny of the animal communities involved in this phenomenon.

Rumen and Fecal Microbiota Characteristics of Qinchuan Cattle with Divergent Residual Feed Intake

Residual feed intake (RFI) is one of the indicators of feed efficiency. To investigate the microbial characteristics and differences in the gastrointestinal tract of beef cattle with different RFI, a metagenome methodology was used to explore the characteristics of the rumen and fecal microbiota in 10 Qinchuan cattle (five in each of the extremely high and extremely low RFI groups). The results of taxonomic annotation revealed that Bacteroidetes and Firmicutes were the most dominant phyla in rumen and feces. Prevotella was identified as a potential biomarker in the rumen of the LRFI group by the LEfSe method, while Turicibacter and Prevotella might be potential biomarkers of the HRFI and LRFI group in feces, respectively. Functional annotation revealed that the microbiota in the rumen of the HRFI group had a greater ability to utilize dietary polysaccharides and dietary protein. Association analysis of rumen microbes (genus level) with host genes revealed that microbiota including Prevotella, Paraprevotella, Treponema, Oscillibacter, and Muribaculum, were significantly associated with differentially expressed genes regulating RFI. This study discovered variances in the microbial composition of rumen and feces of beef cattle with different RFIs, demonstrating that differences in microbes may play a critical role in regulating the bovine divergent RFI phenotype variations.

Gut microbiota and growth performance of offspring are influenced by wet nurse in pigs using cross-fostering trial

BACKGROUND

Nursing mom can regulate the gut microbiome succession in offspring. However, it remains unclear whether these effects are long-term and what effect it has on the growth performance of piglets. This study aimed to develop a cross-fostering model of piglets and investigate the effect of maternal environment on gut microbiota, even the growth performance of the offspring, and if this effect could be maintained in the long term.

RESULTS

Four groups of piglets were generated as follows (n = 12): Duroc piglets nursed by their birth mom (Dd) or Yorkshire sows (Yd), Yorkshire piglets nursed by Duroc sows (Dy) or their birth mom (Yy). The study found that cross-fostering improved the growth performance of piglets for a long time. The gut microbiota of piglets was mainly determined by the breeds of nursing moms before weaning, and it was more and more influenced by their breeds after weaning, but the influence of birth mom breeds still existed. The linear discriminant analysis (LDA) effect size (LEfSe) analysis and Spearman correlation analysis showed that Sutterella, Butyricimonas and Alistipes, which were affected by nursing mom before weaning, had a strong positive correlation with the growth performance of piglets before weaning. Candidatus_Soleaferrea and Treponema, which were affected by both nursing mom and piglet breed after weaning, were significantly negatively correlated with the growth performance of piglets long after weaning.

CONCLUSION

Our results revealed that both the breeds of piglets and their birth moms influence the gut microbiota of piglets for a long time, even after weaning. Additionally, this effect might be related to the growth performance of piglets. © 2022 Society of Chemical Industry.

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.

Exploring variation in the fecal microbial communities of Kasaragod Dwarf and Holstein crossbred cattle

The gut microbiota and its impact on health and nutrition in animals, including cattle has been of intense interest in recent times. Cattle, in particular indigenous varieties like Kasaragod Dwarf cow, have not received the due consideration given to other non-native cattle breeds, and the composition of their fecal microbiome is yet to be established. This study applied 16S rRNA high-throughput sequencing of fecal samples and compared the Kasaragod Dwarf with the highly prevalent Holstein crossbred cattle. Variation in their microbial composition was confirmed by marker gene-based taxonomic analysis. Principle Coordinate Analysis (PCoA) showed the distinct microbial architecture of the two cattle types. While the two cattle types possess unique signature taxa, in Kasaragod Dwarf cattle, many of the identified genera, including Anaerovibrio, Succinivibrio, Roseburia, Coprococcus, Paludibacter, Sutterella, Coprobacillus, and Ruminobacter, have previously been shown to be present in higher abundance in animals with higher feed efficiency. This is the first report of Kasaragod Dwarf cattle fecal microbiome profiling. Our findings highlight the predominance of specific taxa potentially associated with different fermentation products and feed efficiency phenotypes in Kasaragod Dwarf cattle compared to Holstein crossbred cattle.

Disentangling the causal relationship between rabbit growth and cecal microbiota through structural equation models

BACKGROUND

The effect of the cecal microbiome on growth of rabbits that were fed under different regimes has been studied previously. However, the term "effect" carries a causal meaning that can be confounded because of potential genetic associations between the microbiome and production traits. Structural equation models (SEM) can help disentangle such a complex interplay by decomposing the effect on a production trait into direct host genetics effects and indirect host genetic effects that are exerted through microbiota effects. These indirect effects can be estimated via structural coefficients that measure the effect of the microbiota on growth while the effects of the host genetics are kept constant. In this study, we applied the SEM approach to infer causal relationships between the cecal microbiota and growth of rabbits fed under ad libitum (ADG_AL) or restricted feeding (ADG_R).

RESULTS

We identified structural coefficients that are statistically different from 0 for 138 of the 946 operational taxonomic units (OTU) analyzed. However, only 15 and 38 of these 138 OTU had an effect greater than 0.2 phenotypic standard deviations (SD) on ADG_AL and ADG_R, respectively. Many of these OTU had a negative effect on both traits. The largest effects on ADG_R were exerted by an OTU that is taxonomically assigned to the Desulfovibrio genus (- 1.929 g/d, CSS-normalized OTU units) and by an OTU that belongs to the Ruminococcaceae family (1.859 g/d, CSS-normalized OTU units). For ADG_AL, the largest effect was from OTU that belong to the S24-7 family (- 1.907 g/d, CSS-normalized OTU units). In general, OTU that had a substantial effect had low to moderate estimates of heritability.

CONCLUSIONS

Disentangling how direct and indirect effects act on production traits is relevant to fully describe the processes of mediation but also to understand how these traits change before considering the application of an external intervention aimed at changing a given microbial composition by blocking/promoting the presence of a particular microorganism.

Influence of dietary n-3 long-chain fatty acids on microbial diversity and composition of sows' feces, colostrum, milk, and suckling piglets' feces

Introduction

Very little is known about the impact of n-3 long-chain fatty acids (n-3 LCFAs) on the microbiota of sows and their piglets. The aim of this study was to evaluate the effect of n-3 LCFA in sow diets on the microbiota composition of sows' feces, colostrum, and milk as well as that of piglets' feces.

Methods

Twenty-two sows were randomly assigned to either a control or an n-3 LCFA diet from service to weaning. Sows' and piglets' performance was monitored. The gestating and lactating sows' microbiomes in feces, colostrum, and milk were characterized by 16s ribosomal RNA gene sequencing. The fecal microbiome from the two lowest (>800 g) and the two highest birth weight piglets per litter was also characterized, and the LPS levels in plasma were analyzed at weaning.

Results and Discussion

n-3 LCFA increased microbiota alpha diversity in suckling piglets' and gestating sows' feces. However, no effects were observed in colostrum, milk, or lactating sows' feces. Dietary n-3 LCFA modified the microbiota composition of gestating sows' feces, milk, and suckling piglets' feces, without affecting lactating sows' feces or colostrum. In gestating sows' feces and milk, the decrease in genus Succinivibrio and the increase of Proteobacteria phylum, due to the increased genera Brenneria and Escherichia, respectively, stand out. In the feces of suckling piglets, the higher abundance of the beneficial genus Akkermansia and Bacteroides, and different species of Lactobacillus are highlighted. In addition, positive correlations for families and genera were found between lactating sows' feces and milk, milk and suckling piglets' feces, and lactating sows' feces and suckling piglets' feces. To conclude, dietary n-3 LCFA had a positive impact on the microbiome of suckling piglet's feces by increasing microbial diversity and some beneficial bacteria populations, had a few minor modifications on the microbiome of milk and gestating sows' feces and did not change the microbiome in lactating sows' feces or colostrum. Therefore, this study shows the effect of dietary n-3 LCFA on the microbiota of sows, colostrum, milk, and suckling piglets during the lactation period providing crucial information on the microbiota status at the early stages of life, which have an impact on the post-weaning.

Taxonomic and predicted functional signatures reveal linkages between the rumen microbiota and feed efficiency in dairy cattle raised in tropical areas

Ruminants digest plant biomass more efficiently than monogastric animals due to their symbiotic relationship with a complex microbiota residing in the rumen environment. What remains unclear is the relationship between the rumen microbial taxonomic and functional composition and feed efficiency (FE), especially in crossbred dairy cattle (Holstein x Gyr) raised under tropical conditions. In this study, we selected twenty-two F1 Holstein x Gyr heifers and grouped them according to their residual feed intake (RFI) ranking, high efficiency (HE) (n = 11) and low efficiency (LE) (n = 11), to investigate the effect of FE on the rumen microbial taxa and their functions. Rumen fluids were collected using a stomach tube apparatus and analyzed using amplicon sequencing targeting the 16S (bacteria and archaea) and 18S (protozoa) rRNA genes. Alpha-diversity and beta-diversity analysis revealed no significant difference in the rumen microbiota between the HE and LE animals. Multivariate analysis (sPLS-DA) showed a clear separation of two clusters in bacterial taxonomic profiles related to each FE group, but in archaeal and protozoal profiles, the clusters overlapped. The sPLS-DA also revealed a clear separation in functional profiles for bacteria, archaea, and protozoa between the HE and LE animals. Microbial taxa were differently related to HE (e.g., Howardella and Shuttleworthia) and LE animals (e.g., Eremoplastron and Methanobrevibacter), and predicted functions were significatively different for each FE group (e.g., K03395-signaling and cellular process was strongly related to HE animals, and K13643-genetic information processing was related to LE animals). This study demonstrates that differences in the rumen microbiome relative to FE ranking are not directly observed from diversity indices (Faith's Phylogenetic Diversity, Pielou's Evenness, Shannon's diversity, weighted UniFrac distance, Jaccard index, and Bray-Curtis dissimilarity), but from targeted identification of specific taxa and microbial functions characterizing each FE group. These results shed light on the role of rumen microbial taxonomic and functional profiles in crossbred Holstein × Gyr dairy cattle raised in tropical conditions, creating the possibility of using the microbial signature of the HE group as a biological tool for the development of biomarkers that improve FE in ruminants.

Enteroendocrine peptides, growth, and the microbiome during the porcine weaning transition

Background

Growth rate in pigs can be affected by numerous factors that also affect feeding behavior and the microbiome. Recent studies report some communication between the microbiome and the enteroendocrine system. The present study examined if changes in the piglet microbiome between birth and during the weaning transition can be correlated either positively or negatively with growth rate and plasma concentrations of enteroendocrine peptides.

Results

During the post-weaning transition, a 49% reduction in average daily gain was observed at day 24 (P < 0.05) relative to day 21. Pigs recovered by day 28 with body weight and average daily gain increases of 17% and 175%, respectively relative to day 24 and the highest rate of gain was measured at day 35 (462 g/day). The time interval between day 21–24 had the highest number of correlations (n = 25) between the relative abundance differences in taxa over time and corresponding percent weight gain. Amplicon sequence variants with the greatest correlation with percent weight gain between day 21–24 belonged to families Prevotellaceae NK3B31 (ρ = 0.65, P < 0.001), Veillonellaceae (ρ = 0.63, P < 0.001) and Rikenellaceae RC9 (ρ = 0.62, P < 0.001). Seven taxa were positively correlated with percent weight gain between day 24–28. Eight taxa were positively correlated with percent weight gain between day 28–35, of which four were Clostridia. Only Lactobacillus reuteri was positively correlated across both day 24–28 and day 28–35 analyses. Insulin-like growth factor 1 (IGF-1; R2 = 0.61, P < 0.001), glucose-dependent insulinotropic polypeptide (GIP; R2 = 0.20, P < 0.001), glucagon-like peptide 1 (GLP-1; R2 = 0.51, P < 0.001), and glucagon-like peptide 2 (GLP-2; R2 = 0.21, P < 0.001) were significantly associated with the piglet fecal community NMDS, while serotonin showed no significant association (R2 = 0.03, P = 0.15). Higher concentrations of GLP-1 and GLP-2 characterized day 1 fecal communities, while GIP levels had the strongest relationship primarily with samples ordinated with the day 21 cluster.

Conclusions

Demonstration of an association of certain taxa with individual gut peptides at specific ages suggests the potential for the microbiome to elicit changes in the gut enteroendocrine system during early postnatal development in the pig.

Effect of host genetics and gut microbiome on fat deposition traits in pigs

Fat deposition affects meat quality, flavor, and production in pigs. Fat deposition is influenced by both genetics and environment. Symbiotic microbe with the host is an important environmental factor to influence fat deposition. In this study, the fat deposition traits were measured in 239 individuals obtained from Tongcheng pigs × Large White pigs resource population. The interactions between genetics and gut microbiome in fat deposition traits were investigated through whole-genome sequencing and cecum microbial 16S ribosomal RNA sequencing. The results showed that the percentage of leaf fat (PL) and intramuscular fat content (IMF) were significantly influenced by host genetics–gut microbiome interaction. The effects of interactions between host genetics and gut microbiome on PL and IMF were 0.13 and 0.29, respectively. The heritability of PL and IMF was estimated as 0.71 and 0.89, respectively. The microbiability of PL and IMF was 0.20 and 0.26, respectively. Microbiome-wide association analysis (MWAS) revealed Anaeroplasma, Paraprevotella, Pasteurella, and Streptococcus were significantly associated with PL, and Sharpea and Helicobacter exhibited significant association with IMF (p &lt; 0.05). Furthermore, Paraprevotella was also identified as a critical microbe affecting PL based on the divergent Wilcoxon rank-sum test. Overall, this study reveals the effect of host genetics and gut microbiome on pig fat deposition traits and provides a new perspective on the genetic improvement of pig fat deposition traits.

Gut microbiota and host genetics contribute to the phenotypic variation of digestive and feed efficiency traits in growing pigs fed a conventional and a high fiber diet

Background

Breeding pigs that can efficiently digest alternative diets with increased fiber content is a viable strategy to mitigate the feed cost in pig production. This study aimed at determining the contribution of the gut microbiota and host genetics to the phenotypic variability of digestive efficiency (DE) traits, such as digestibility coefficients of energy, organic matter and nitrogen, feed efficiency (FE) traits (feed conversion ratio and residual feed intake) and growth traits (average daily gain and daily feed intake). Data were available for 791 pigs fed a conventional diet and 735 of their full-sibs fed a high-fiber diet. Fecal samples were collected at 16 weeks of age to sequence the V3–V4 regions of the 16S ribosomal RNA gene and predict DE with near-infrared spectrometry. The proportions of phenotypic variance explained by the microbiota (microbiability) were estimated under three OTU filtering scenarios. Then, microbiability and heritability were estimated independently (models Micro and Gen) and jointly (model Micro+Gen) using a Bayesian approach for all traits. Breeding values were estimated in models Gen and Micro+Gen.

Results

Differences in microbiability estimates were significant between the two extreme filtering scenarios (14,366 and 803 OTU) within diets, but only for all DE. With the intermediate filtering scenario (2399 OTU) and for DE, microbiability was higher (> 0.44) than heritability (< 0.32) under both diets. For two of the DE traits, microbiability was significantly higher under the high-fiber diet (0.67 ± 0.06 and 0.68 ± 0.06) than under the conventional diet (0.44 ± 0.06). For growth and FE, heritability was higher (from 0.26 ± 0.06 to 0.44 ± 0.07) than microbiability (from 0.17 ± 0.05 to 0.35 ± 0.06). Microbiability and heritability estimates obtained with the Micro+Gen model did not significantly differ from those with the Micro and Gen models for all traits. Finally, based on their estimated breeding values, pigs ranked differently between the Gen and Micro+Gen models, only for the DE traits under both diets.

Conclusions

The microbiota explained a significant proportion of the phenotypic variance of the DE traits, which was even larger than that explained by the host genetics. Thus, the use of microbiota information could improve the selection of DE traits, and to a lesser extent, of growth and FE traits. In addition, our results show that, at least for DE traits, filtering OTU is an important step and influences the microbiability.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00742-6.

Effects of High Ambient Temperature on Small Intestinal Morphology and Colonic Microbiota in Weaned Piglets

A total of 16 crossbred (Duroc × Landrace × Yorkshire) barrows, with an average initial body weight of 8.61 ± 0.24 kg (28 days of age), were randomly allotted into the control group (CON group) and high ambient temperature group (HT group) with 8 replicates per group, 1 pig per replicate. The ambient temperature of the CON group was controlled at 26 ± 1 °C, and the HT group was controlled at 35 ± 1 °C. The study lasted for 21 days. Our results showed that high ambient temperature significantly decreased the average daily feed intake (ADFI) and average daily gain (ADG) of piglets (p < 0.05), and the feed-to-gain ratio was significantly increased (p < 0.05). The liver index, spleen index, and thymus index of piglets in the HT group were significantly decreased (p < 0.05). The villous height (VH) of the duodenum, jejunum, and ileum of piglets in the HT group was significantly decreased (p < 0.05), whereas the crypt depth (CD) of the duodenum was significantly increased (p < 0.05), and the VH-to-CD ratio of the duodenum and ileum was significantly decreased (p < 0.05). The piglets in the HT group showed a higher (p < 0.05) observed-species index, PD whole tree index, and Shannon index, indicating that there was a significant difference in species richness and diversity between the two groups. At the genus level, the piglets in the HT group showed a greater (p < 0.05) percent of Desulfovibrio, Occillibater, and Catenisphaera. HT reduced glycan biosynthesis and metabolism, transport and catabolism, lipid metabolism, amino acids metabolism, secondary metabolites biosynthesis, aging, endocrine system, signaling molecules, and interaction of colon microbiota (p < 0.05), and increased signal transduction, cell motility, transcription, and genetic information processing (p < 0.05).

Tryptophan Supplementation Enhances Intestinal Health by Improving Gut Barrier Function, Alleviating Inflammation, and Modulating Intestinal Microbiome in Lipopolysaccharide-Challenged Piglets

Tryptophan (Trp) can modify the gut microbiota. However, there is no information about the effect of Trp on intestinal microbiota after lipopolysaccharide (LPS) challenge. This study aimed to investigate the effect of Trp on intestinal barrier function, inflammation, antioxidant status, and microbiota in LPS-challenged piglets. A total of 18 weaned castrated piglets were randomly divided into three treatments with 6 replicate per treatment, namely, (i) non-challenged control (CON); (ii) LPS-challenged control (LPS-CON); and (iii) LPS + 0.2% Trp (LPS-Trp). After feeding with control or 0.2% tryptophan-supplemented diets for 35 days, pigs were intraperitoneally injected with LPS (100 μg/kg body weight) or saline. At 4 h post-challenge, all pigs were slaughtered, and colonic samples were collected. The samples were analyzed for gut microbiota, fatty acids, antioxidant parameters, and the expression of mRNA and protein. The community bar chart showed that Trp supplementation to LPS-challenged pigs increased the relative abundance of Anaerostipes (P < 0.05) and tended to increase the relative abundance of V9D2013_group (P = 0.09), while decreased the relative abundance of Corynebacterium (P < 0.05) and unclassified_c__Bacteroidia (P < 0.01). Gas chromatography showed that Trp increased the concentrations of acetate, propionate, butyrate, and isovalerate in the colonic digesta (P < 0.05). Trp reduced the mRNA level of pro-inflammatory cytokines (P < 0.01), and increased mRNA level of aryl hydrocarbon receptor, cytochrome P450 (CYP) 1A1 and CYP1B1 (P < 0.05). Correlation analysis results showed that acetate, propionate, and butyrate concentrations were positively correlated with mRNA level of occludin and CYP1B1 (P < 0.05), and were negatively correlated with pro-inflammatory cytokines gene expression (P < 0.05). Isovalerate concentration was positively correlated with catalase activity (P < 0.05), and was negatively correlated with pro-inflammatory cytokines gene expression (P < 0.05). Furthermore, Trp enhanced the antioxidant activities (P < 0.01), and increased mRNA and protein expressions of claudin-1, occludin, and zonula occludens-1 (P < 0.01) after LPS challenge. These results suggest that Trp enhanced intestinal health by a modulated intestinal microbiota composition, improved the short chain fatty acids synthesis, reduced inflammation, increased antioxidant capacity, and improved intestinal barrier function.

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.

Stool and Ruminal Microbiome Components Associated With Methane Emission and Feed Efficiency in Nelore Beef Cattle

Background: The impact of extreme changes in weather patterns on the economy and human welfare is one of the biggest challenges our civilization faces. From anthropogenic contributions to climate change, reducing the impact of farming activities is a priority since it is responsible for up to 18% of global greenhouse gas emissions. To this end, we tested whether ruminal and stool microbiome components could be used as biomarkers for methane emission and feed efficiency in bovine by studying 52 Brazilian Nelore bulls belonging to two feed intervention treatment groups, that is, conventional and by-product-based diets.

Results: We identified a total of 5,693 amplicon sequence variants (ASVs) in the Nelore bulls’ microbiomes. A Differential abundance analysis with the ANCOM approach identified 30 bacterial and 15 archaeal ASVs as differentially abundant (DA) among treatment groups. An association analysis using Maaslin2 software and a linear mixed model indicated that bacterial ASVs are linked to the host’s residual methane emission (RCH₄) and residual feed intake (RFI) phenotype variation, suggesting their potential as targets for interventions or biomarkers.

Conclusion: The feed composition induced significant differences in both abundance and richness of ruminal and stool microbial populations in ruminants of the Nelore breed. The industrial by-product-based dietary treatment applied to our experimental groups influenced the microbiome diversity of bacteria and archaea but not of protozoa. ASVs were associated with RCH₄ emission and RFI in ruminal and stool microbiomes. While ruminal ASVs were expected to influence CH₄ emission and RFI, the relationship of stool taxa, such as Alistipes and Rikenellaceae (gut group RC9), with these traits was not reported before and might be associated with host health due to their link to anti-inflammatory compounds. Overall, the ASVs associated here have the potential to be used as biomarkers for these complex phenotypes.

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.

Microbiability and microbiome-wide association analyses of feed efficiency and performance traits in pigs

Background

The objective of the present study was to investigate how variation in the faecal microbial composition is associated with variation in average daily gain (ADG), backfat thickness (BFT), daily feed intake (DFI), feed conversion ratio (FCR), and residual feed intake (RFI), using data from two experimental pig lines that were divergent for feed efficiency. Estimates of microbiability were obtained by a Bayesian approach using animal mixed models. Microbiome-wide association analyses (MWAS) were conducted by single-operational taxonomic units (OTU) regression and by back-solving solutions of best linear unbiased prediction using a microbiome covariance matrix. In addition, accuracy of microbiome predictions of phenotypes using the microbiome covariance matrix was evaluated.

Results

Estimates of heritability ranged from 0.31 ± 0.13 for FCR to 0.51 ± 0.10 for BFT. Estimates of microbiability were lower than those of heritability for all traits and were 0.11 ± 0.09 for RFI, 0.20 ± 0.11 for FCR, 0.04 ± 0.03 for DFI, 0.03 ± 0.03 for ADG, and 0.02 ± 0.03 for BFT. Bivariate analyses showed a high microbial correlation of 0.70 ± 0.34 between RFI and FCR. The two approaches used for MWAS showed similar results. Overall, eight OTU with significant or suggestive effects on the five traits were identified. They belonged to the genera and families that are mainly involved in producing short-chain fatty acids and digestive enzymes. Prediction accuracy of phenotypes using a full model including the genetic and microbiota components ranged from 0.60 ± 0.19 to 0.78 ± 0.05. Similar accuracies of predictions of the microbial component were observed using models that did or did not include an additive animal effect, suggesting no interaction with the genetic effect.

Conclusions

Our results showed substantial associations of the faecal microbiome with feed efficiency related traits but negligible effects with growth traits. Microbiome data incorporated as a covariance matrix can be used to predict phenotypes of animals that do not (yet) have phenotypic information. Connecting breeding environment between training sets and predicted populations could be necessary to obtain reliable microbiome predictions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00717-7.

Exploring the Intestinal Microbiota and Metabolome Profiles Associated With Feed Efficiency in Pacific Abalone (Haliotis discus hannai)

Feed efficiency (FE) is critical to the economic and environmental benefits of aquaculture. Both the intestines and intestinal microbiota play a key role in energy acquisition and influence FE. In the current research, intestinal microbiota, metabolome, and key digestive enzyme activities were compared between abalones with high [Residual feed intake (RFI) = -0.029] and low FE (RFI = 0.022). The FE of group A were significantly higher than these of group B. There were significant differences in intestinal microbiota structures between high- and low-FE groups, while higher microbiota diversity was observed in the high-FE group. Differences in FE were also strongly correlated to variations in intestinal digestive enzyme activity that may be caused by Pseudoalteromonas and Cobetia. In addition, Saprospira, Rhodanobacteraceae, Llumatobacteraceae, and Gaiellales may potentially be utilized as biomarkers to distinguish high- from low-FE abalones. Significantly different microorganisms (uncultured beta proteobacterium, BD1_7_clade, and Lautropia) were found to be highly correlated to significantly different metabolites [DL-methionine sulfoxide Arg-Gln, L-pyroglutamic acid, dopamine, tyramine, phosphatidyl cholines (PC) (16:0/16:0), and indoleacetic acid] in the high- and low-FE groups, and intestinal trypsin activity also significantly differed between the two groups. We propose that interactions occur among intestinal microbiota, intestinal metabolites, and enzyme activity, which improve abalone FE by enhancing amino acid metabolism, immune response, and signal transduction pathways. The present study not only elucidates mechanisms of variations in abalone FE, but it also provides important basic knowledge for improving abalone FE by modulating intestinal microbiota.

Different Alterations in Gut Microbiota between Bifidobacterium longum and Fecal Microbiota Transplantation Treatments in Propionic Acid Rat Model of Autism

Autism spectrum disorders (ASD) consist of a range of neurodevelopmental conditions accompanied by dysbiosis of gut microbiota. Therefore, a number of microbiota manipulation strategies were developed to restore their balance. However, a comprehensive comparison of the various methods on gut microbiota is still lacking. Here, we evaluated the effect of Bifidobacterium (BF) treatment and fecal microbiota transplantation (FT) on gut microbiota in a propionic acid (PPA) rat model of autism using 16S rRNA sequencing. Following PPA treatment, gut microbiota showed depletion of Bacteroidia and Akkermansia accompanied by a concomitant increase of Streptococcus, Lachnospiraceae, and Paraeggerthella. The dysbiosis was predicted to cause increased levels of porphyrin metabolism and impairments of acyl-CoA thioesterase and ubiquinone biosynthesis. On the contrary, BF and FT treatments resulted in a distinct increase of Clostridium, Bifidobacterium, Marvinbryantia, Butyricicoccus, and Dorea. The taxa in BF group positively correlated with vitamin B12 and flagella biosynthesis, while FT mainly enriched flagella biosynthesis. In contrast, BF and FT treatments negatively correlated with succinate biosynthesis, pyruvate metabolism, nitrogen metabolism, beta-Lactam resistance, and peptidoglycan biosynthesis. Therefore, the present study demonstrated that BF and FT treatments restored the PPA-induced dysbiosis in a treatment-specific manner.

FI: The Fecobiome Initiative

Animal husbandry has been key to the sustainability of human societies for millennia. Livestock animals, such as cattle, convert plants to protein biomass due to a compartmentalized gastrointestinal tract (GIT) and the complementary contributions of a diverse GIT microbiota, thereby providing humans with meat and dairy products. Research on cattle gut microbial symbionts has mainly focused on the rumen (which is the primary fermentation compartment) and there is a paucity of functional insight on the intestinal (distal end) microbiota, where most foodborne zoonotic bacteria reside. Here, we present the Fecobiome Initiative (or FI), an international effort that aims at facilitating collaboration on research projects related to the intestinal microbiota, disseminating research results, and increasing public availability of resources. By doing so, the FI can help mitigate foodborne and animal pathogens that threaten livestock and human health, reduce the emergence and spread of antimicrobial resistance in cattle and their proximate environment, and potentially improve the welfare and nutrition of animals. We invite all researchers interested in this type of research to join the FI through our website: www.fecobiome.com

Intestinal microbiota modulation and improved growth in pigs with post-weaning antibiotic and ZnO supplementation but only subtle microbiota effects with Bacillus altitudinis

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

Resistant starch: Implications of dietary inclusion on gut health and growth in pigs: a review

Starch from cereal grains, pulse grains, and tubers is a major energy substrate in swine rations constituting up to 55% of the diet. In pigs, starch digestion is initiated by salivary and then pancreatic α-amylase, and has as final step the digestion of disaccharides by the brush-border enzymes in the small intestine that produce monosaccharides (glucose) for absorption. Resistant starch (RS) is the proportion of starch that escapes the enzymatic digestion and absorption in the small intestine. The undigested starch reaches the distal small intestine and hindgut for microbial fermentation, which produces short-chain fatty acids (SCFA) for absorption. SCFA in turn, influence microbial ecology and gut health of pigs. These fermentative metabolites exert their benefits on gut health through promoting growth and proliferation of enterocytes, maintenance of intestinal integrity and thus immunity, and modulation of the microbial community in part by suppressing the growth of pathogenic bacteria while selectively enhancing beneficial microbes. Thus, RS has the potential to confer prebiotic effects and may contribute to the improvement of intestinal health in pigs during the post-weaning period. Despite these benefits to the well-being of pigs, RS has a contradictory effect due to lower energetic efficiency of fermented vs. digested starch absorption products. The varying amount and type of RS interact differently with the digestion process along the gastrointestinal tract affecting its energy efficiency and host physiological responses including feed intake, energy metabolism, and feed efficiency. Results of research indicate that the use of RS as prebiotic may improve gut health and thereby, reduce the incidence of post-weaning diarrhea (PWD) and associated mortality. This review summarizes our current knowledge on the effects of RS on microbial ecology, gut health and growth performance in pigs.

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.

Reduced Feeding Frequency Improves Feed Efficiency Associated With Altered Fecal Microbiota and Bile Acid Composition in Pigs

A biphasic feeding regimen exerts an improvement effect on feed efficiency of pigs. While gut microbiome and metabolome are known to affect the host phenotype, so far the effects of reduced feeding frequency on fecal microbiota and their metabolism in pigs remain unclear. Here, the combination of 16S rRNA sequencing technique as well as untargeted and targeted metabolome analyses was adopted to investigate the fecal microbiome and metabolome of growing–finishing pigs in response to a biphasic feeding [two meals per day (M2)] pattern. Sixty crossbred barrows were randomly assigned into two groups with 10 replicates (three pigs/pen), namely, the free-access feeding group (FA) and the M2 group. Pigs in the FA group were fed free access while those in the M2 group were fed ad libitum twice daily for 1 h at 8:00 and 18:00. Results showed that pigs fed biphasically exhibited increased feed efficiency compared to FA pigs. The Shannon and Simpson indexes were significantly increased by reducing the feeding frequency. In the biphasic-fed pigs, the relative abundances of Subdoligranulum, Roseburia, Mitsuokella, and Terrisporobacter were significantly increased while the relative abundances of unidentified_Spirochaetaceae, Methanobrevibacter, unidentified_Bacteroidales, Alloprevotella, Parabacteroides, and Bacteroides were significantly decreased compared to FA pigs. Partial least-square discriminant analysis (PLS-DA) analysis revealed an obvious variation between the FA and M2 groups; the differential features were mainly involved in arginine, proline, glycine, serine, threonine, and tryptophan metabolism as well as primary bile acid (BA) biosynthesis. In addition, the changes in the microbial genera were correlated with the differential fecal metabolites. A biphasic feeding regimen significantly increased the abundances of primary BAs and secondary BAs in feces of pigs, and the differentially enriched BAs were positively correlated with some specific genera. Taken together, these results suggest that the improvement effect of a reduced feeding frequency on feed efficiency of pigs might be associated with the altered fecal microbial composition and fecal metabolite profile in particular the enlarged stool BA pool.

Disinfection of Maternal Environments Is Associated with Piglet Microbiome Composition from Birth to Weaning

Maternal factors predetermine offspring development and health, including the establishment of offsprings' first microbiomes. Research in swine has shown that early microbial exposures impact microbiome colonization in piglets, but this phenomenon has never been tested in the context of delivery room disinfection. Thus, we exposed gestating sows to two delivery environments (n = 3/environment): stalls cleaned with a broad-spectrum disinfectant (disinfected environment [D]) or stalls cleaned only with hot-water power washing (nondisinfected environment [Nde]), 3 days prior to farrowing. Microbiomes of sows and farrowed piglets (n = 27/environment) were profiled at 4 different time points from birth to weaning via 16S rRNA sequencing. The results show that although vaginal, milk, skin, and gut microbiomes in mothers were minimally affected, sanitation of farrowing stalls impacted piglet microbiome colonization. These effects were mainly characterized by lower bacterial diversity in the gut and nasal cavity, specifically in D piglets at birth, and by distinct taxonomic compositions from birth to weaning depending on the farrowing environment. For instance, environmental bacteria greatly influenced microbiome colonization in Nde piglets, which also harbored significantly higher abundances of gut Lactobacillus and nasal Enhydrobacter at several time points through weaning. Different sanitation strategies at birth also resulted in distinct microbiome assembly patterns, with lower microbial exposures in D piglets being associated with limited interactions between bacterial taxa. However, increasing microbial exposures at birth through the lack of disinfection were also associated with lower piglet weight, highlighting the importance of understanding the trade-offs among optimal microbiome development, health, and growth performance in swine production systems. IMPORTANCE We show that levels of disinfection in farrowing facilities can impact early microbial exposures and colonization by pioneer microbes in piglets. Although previous research has shown a similar effect by raising pigs outdoors or by exposing them to soil, these practices are unattainable in most swine production systems in the United States due to biosecurity practices. Thus, our results underscore the importance of evaluating different disinfection practices in swine production to safely reduce pathogenic risks without limiting early microbial exposures. Allowing early exposure to both beneficial and pathogenic microbes may positively impact immune responses, reduce the stressors of weaning, and potentially reduce the need for dietary antimicrobials. However, the benefits of modified early microbial exposures need to be accomplished along with acceptable growth performance. Thus, our results also provide clues for understanding how disinfection practices in farrowing rooms may impact early microbiome development and assembly.

Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs

BACKGROUND

The gut microbiota influences host performance playing a relevant role in homeostasis and function of the immune system. The aim of the present work was to identify microbial signatures linked to immunity traits and to characterize the contribution of host-genome and gut microbiota to the immunocompetence in healthy pigs.

RESULTS

To achieve this goal, we undertook a combination of network, mixed model and microbial-wide association studies (MWAS) for 21 immunity traits and the relative abundance of gut bacterial communities in 389 pigs genotyped for 70K SNPs. The heritability (h2; proportion of phenotypic variance explained by the host genetics) and microbiability (m2; proportion of variance explained by the microbial composition) showed similar values for most of the analyzed immunity traits, except for both IgM and IgG in plasma that was dominated by the host genetics, and the haptoglobin in serum which was the trait with larger m2 (0.275) compared to h2 (0.138). Results from the MWAS suggested a polymicrobial nature of the immunocompetence in pigs and revealed associations between pigs gut microbiota composition and 15 of the analyzed traits. The lymphocytes phagocytic capacity (quantified as mean fluorescence) and the total number of monocytes in blood were the traits associated with the largest number of taxa (6 taxa). Among the associations identified by MWAS, 30% were confirmed by an information theory network approach. The strongest confirmed associations were between Fibrobacter and phagocytic capacity of lymphocytes (r = 0.37), followed by correlations between Streptococcus and the percentage of phagocytic lymphocytes (r = -0.34) and between Megasphaera and serum concentration of haptoglobin (r = 0.26). In the interaction network, Streptococcus and percentage of phagocytic lymphocytes were the keystone bacterial and immune-trait, respectively.

CONCLUSIONS

Overall, our findings reveal an important connection between gut microbiota composition and immunity traits in pigs, and highlight the need to consider both sources of information, host genome and microbial levels, to accurately characterize immunocompetence in pigs.

Microbial Quality of Liquid Feed for Pigs and Its Impact on the Porcine Gut Microbiome

Simple Summary

Liquid feed is produced by mixing dry feed ingredients with water, and sometimes liquid co-products from the food and beverage industry, at a defined ratio. Liquid feeding of pigs is popular, particularly in parts of northern and western Europe, and can be associated with lower feed costs, improved dry matter intake, growth rate and gut health, compared to dry feeding. However, spontaneous/uncontrolled fermentation upon mixing of feed with water or co-products can decrease the microbial and nutritional quality of the feed, resulting in poorer pig health and growth. For this reason, strategies aimed at optimising liquid feed microbial quality are frequently employed. These include: deliberate fermentation with/without the use of lactic acid bacteria starter cultures that produce lactic acid and lower the feed pH, thereby preventing growth of pathogens. Fermenting only the cereal component of the diet is preferred to whole diet fermentation to minimise loss of free amino acids from the diet during fermentation. This review examines the microbiome of liquid feed and explores how optimisation strategies impact both feed microbial quality and the gut microbiota and growth of liquid-fed pigs. It also covers cleaning and disinfection of liquid feeding systems and how this might impact liquid feed microbial quality.

Abstract

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

A mix of functional amino acids and grape polyphenols promotes the growth of piglets, modulates the gut microbiota in vivo and regulates epithelial homeostasis in intestinal organoids

Weaning is a challenging period for gut health in piglets. Previous studies showed that dietary supplementations with either amino acids or polyphenols promote piglet growth and intestinal functions, when administered separately. Thus, we hypothesized that a combination of amino acids and polyphenols could facilitate the weaning transition. Piglets received during the first two weeks after weaning a diet supplemented or not with a mix of a low dose (0.1%) of functional amino acids (L-arginine, L-leucine, L-valine, L-isoleucine, L-cystine) and 100 ppm of a polyphenol-rich extract from grape seeds and skins. The mix of amino acids and polyphenols improved growth and feed efficiency. These beneficial effects were associated with a lower microbiota diversity and a bloom of Lactobacillaceae in the jejunum content while the abundance of Proteobacteria was reduced in the caecum content. The mix of amino acids and polyphenols also increased the production by the caecum microbiota of short-chain fatty acids (butyrate, propionate) and of metabolites derived from amino acids (branched-chain fatty acids, valerate, putrescine) and from polyphenols (3-phenylpropionate). Experiments in piglet jejunum organoids revealed that the mix of amino acids and polyphenols upregulated the gene expression of epithelial differentiation markers while it reduced the gene expression of proliferation and innate immunity markers. In conclusion, the supplementation of a mix of amino acids and polyphenols is a promising nutritional strategy to manage gut health in piglets through the modulation of the gut microbiota and of the epithelial barrier.

The Impact of Genetics on Gut Microbiota of Growing and Fattening Pigs under Moderate N Restriction

Characterization of intestinal microbiota is of great interest due to its relevant impact on growth, feed efficiency and pig carcass quality. Microbial composition shifts along the gut, but it also depends on the host (i.e., age, genetic background), diet composition and environmental conditions. To simultaneously study the effects of producing type (PT), production phase (PP) and dietary crude protein (CP) content on microbial populations, 20 Duroc pigs and 16 crossbred pigs (F2), belonging to growing and fattening phases, were used. Half of the pigs of each PT were fed a moderate CP restriction (2%). After sacrifice, contents of ileum, cecum and distal colon were collected for sequencing procedure. Fattening pigs presented higher microbial richness than growing pigs because of higher maturity and stability of the community. The F2 pigs showed higher bacterial alpha diversity and microbial network complexity (cecum and colon), especially in the fattening phase, while Duroc pigs tended to have higher Firmicutes/Bacteroidetes ratio in cecum segment. Lactobacillus was the predominant genus, and along with Streptococcus and Clostridium, their relative abundance decreased throughout the intestine. Although low CP diet did not alter the microbial diversity, it increased interaction network complexity. These results have revealed that the moderate CP restriction had lower impact on intestinal microbiota than PP and PT of pigs.