Probiotic roles of Lactobacillus sp. in swine: insights from gut microbiota

The dual action of probiotic lactobacilli in suppressing virulence and survival of Arcobacter butzleri

Arcobacter butzleri is a widely distributed foodborne and waterborne pathogen, increasingly recognized as an emerging enteropathogen. Understanding its survival mechanisms and interactions with probiotics is crucial for developing targeted intervention strategies. A. butzleri must withstand various hostile conditions to successfully colonize the gastrointestinal tract, including inhibition by probiotics, such as Limosilactobacillus reuteri, Lactobacillus acidophilus and Lactiplantibacillus plantarum. Thus, this study aimed to assess the survival of A. butzleri under acidic conditions and determine its minimum inhibitory concentration (MIC) for bile salts. Additionally, the antimicrobial potential of the lactobacilli strains was evaluated by analysing the effects of their culture-free supernatant (CFS) on A. butzleri growth, coculture interactions, and biofilm formation. The influence of lactobacilli on A. butzleri was further investigated through competition, displacement and exclusion assays using Caco-2 cell models. The results indicate that lactobacilli strains exhibit tolerance to acidic environments and physiological bile salt concentrations, whereas A. butzleri was more susceptible to acidic stress. The antagonistic effect of lactobacilli was evidenced by growth inhibition of A. butzleri in the presence of CFS or during coculture. However, CFS from certain lactobacilli strains was found to enhance biofilm formation, highlighting potential consequences. Furthermore, while lactobacilli did not demonstrate significant antagonistic effects in competition assays, they effectively displaced and excluded A. butzleri in the Caco-2 infection model. Overall, these findings suggest that probiotic lactobacilli can inhibit A. butzleri growth, yet their impact on its virulence remains uncertain. This underscores the need for strain-specific probiotic selection to effectively target this pathogen and emphasizes that not every probiotic contribute to the prevention of A. butzleri infections.

Local, environmental and trace metal effects on gut microbiota diversity in urban feral pigeons

Nowadays, understanding the biotic responses to the enhanced urbanization need to encompass not the only the physiological and phenotypic features but also the related microbiota of wildlife animals. One of main threats in urban ecosystems is the chemical pollution. Thus, we have explored whether the cloacal microbiota of feral pigeons (Columba livia) is impacted by both their geographical foraging area, and metal exposure in an urban context. First, pigeons were captured in 4 specific areas of Paris (France) and placed in captivity. By applying a 16SrRNA metabarcoding approach, we observed that the gut microbiota diversity was structured according to the capture sites, with strong variation of Actinobacteria, Bacilli and Clostridia, that could be linked to the granivorous or low-protein diets. Subsequently, we experimentally exposed these pigeons to zinc and/or lead (two-factor cross design) during 90 days in a non-urban environment, but no impact on the composition nor diversity of pigeon gut microbiota, has been observed after 45 and 90 days of metal exposures. However, the composition and diversity significantly differed from the microbiota at the capture period, with the emergence of taxa belonging to Corynebacterium and Bifidobacterium in captive conditions. These data highlight a strong impact of the lifestyles (captivity in non-urban environment) on the gut microbiota composition. In parallel, we hypothesized that the diet and the local environment might have smoothed the impact of the metal exposure for pigeons that could quickly change the structure of their gut microbiota. Our findings shed light on the effects of urban pollution and environment on bird communities, that can be extended to their gut microbiota causing potential additive or synergic negative effects to host organisms and populations.

Colonic bacterial community responding to selenium-enriched yeast supplementation associated with improved gut mucus function in growing-finishing pigs

Selenium-enriched yeast (SeY), a high-quality organic source of selenium, enhances antioxidant activity and intestinal health in swine. This study aims to evaluate the effects of varying dietary SeY levels on intestinal morphology, epithelial mucus production, antioxidant activity, and colonic bacterial communities in growing-finishing pigs. Thirty 90-day-old Duroc×Landrace×Yorkshire growing-finishing pigs (average body weight of 54.37±2.13 kg) were randomly assigned to five treatment groups. The control group (CON) was fed a basal diet, while the other four groups were fed the basal diet supplemented with SeY at 0.3, 1, 3, and 5 mg/kg, respectively, for an 80-day of feeding trial. The results showed that the addition of SeY at 0.3 mg/kg increased villus height, villus height/crypt ratio, and mucus production in the ileum, as evidenced by the increase in goblet cell number and mucus thickness (P < 0.05). Furthermore, 0.3 mg/kg SeY up-regulated the mRNA expression levels of the MUC-1, claudin-1, occludin, and ZO-1 genes (P < 0.05). In contrast, high-dose SeY at 5 mg/kg resulting in damage to mucosal morphology. Ileal antioxidant activity of SOD and GSH-Px, and jejunal mRNA expression of GPX-1 and GPX-4, were higher in response to SeY (P < 0.05). Faecal Se excretion increased in SeY groups in a dose-dependent manner (P < 0.05). SeY led to a significant difference in beta diversity among treatment groups (P = 0.002) and led to a significant decrease in the concentrations of isobutyric and isovaleric acids when compared to the control group (P < 0.05). The acetate, propionate, butyrate, and total short-chain fatty acids were positively correlated with the biomarker genera Agathobacter (SeY at 0.3mg/kg), while isobutyrate and isovalerate were negatively correlated with biomarker genera Lactobacillus (SeY at 0.3mg/kg) (P < 0.05). Faecal accumulation of Se was positively correlated with the biomarker genera Alloprevotella (SeY at 3mg/kg) and Prevotellaceae_UCG-001 (SeY at 5mg/kg) and was negatively correlated with biomarker genera Agathobacter (SeY at 0.3mg/kg), Bacteroides (CON), and Faecalibacterium (CON) (P < 0.05). In conclusion, SeY doses of 0.3 mg/kg have beneficial effects on intestinal health, whereas prolonged SeY doses up to 5 mg/kg may compromise the intestinal mucus function in growing-finishing pigs.

Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status

BACKGROUND

Antibiotics are used in animal husbandry to control infectious diseases. Different stressors can compromise animal health, leaving piglets vulnerable to pathogens, especially enterotoxigenic Escherichia coli (ETEC), which causes post-weaning diarrhoea (PWD), the major source of mortality and morbidity in swine production. Furthermore, PWD is a recurrent disease for certain farms, suggesting a link between gut microbial composition and animal health. The aim of this study was to identify the intestinal microbiota of pigs on farms with high health status (HHS) and low health status (LHS) to determine the relationships between sanitary status and gut health. Therefore, three pig farms with LHS presenting recurrent problems of PWD and three farms with HHS were selected to characterise the intestinal microbiome of sows and their piglets. 16 S rRNA gene sequencing technology was used to determine the associations of the gut microbiome with health. With the aim of bringing the MinION Nanopore device to the field for its portability and taxonomic resolution, the results obtained with Illumina were compared to those obtained with Nanopore.

RESULTS

Overall, the results indicated remarkable differences in intestinal microbial communities between animals from LHS farms and those from HHS farms, suggesting that the microbiomes of LHS animals were enriched with potential pathogenic microorganisms, mainly from the Pseudomonadota phylum, such as the genus Escherichia-Shigella, and their associated related species. Moreover, animals from HHS were enriched with beneficial microorganisms, such as Lactobacillus spp., Christensenellaceae R7 group, Treponema, Acetitomaculum and Oscillospiraceae UCG-005.

CONCLUSIONS

This study identifies potential microorganisms that may contribute to health and disease in pig farms with HHS and LHS, suggesting that tracking their occurrence might provide insight into sanitary conditions. Moreover, this research highlights the compatibility between Illumina and Nanopore sequencing platforms, justifying the use of MinION Nanopore device in field applications for in situ studies of PWD. This application has the potential to enhance sustainable economic growth in swine farms by enabling more effective monitoring and management of animal health.

Influence of host-specific and locally isolated multi-strain probiotics on piglet performance, mortality, inflammatory response, and gut microbiome

OBJECTIVE

This study aimed to assess the impact of host-specific and locally isolated multistrain probiotics on piglet performance, mortality, inflammatory responses, and gut microbiome.

METHODS

A total of 52 piglet litters-34 from Landrace sows and 18 from Large White sows-were allocated to two groups: a control group and a multi-strain probiotic group. The probiotic group comprised seven strains of lactic acid bacteria (MLAB): Lactobacillus brevis, Lactobacillus reuteri, Lactobacillus paraplantarum, Lactococcus lactis, Lactobacillus pentosus, Weissella cibaria, and Pediococcus pentosaceus. Each strain was included in equal concentrations, resulting in a final liquid mixture containing 109 colony forming units/mL. The MLAB group received the probiotics orally starting from 7 days of age until weaning at four weeks. Following weaning, supplementation continued via feed spraying for an additional four weeks.

RESULTS

MLAB supplementation did not significantly affect piglet performance but showed a trend towards reducing the mortality rate (p = 0.06). It influenced the inflammatory response by upregulating the expression of anti-inflammatory cytokines interleukin (IL)-4 and IL-10 (p<0.05). Microbial community analysis indicated that MLAB supplementation increased both microbial diversity (Simpson index: p = 0.06) and species richness (Chao1 index: p = 0.02). Piglets receiving MLAB had a significantly higher abundance of the phylum Firmicutes (p<0.01) compared to the control group, while the abundance of the phylum Bacteroidota was markedly reduced (p<0.01). In addition, the relative abundance of the bacterial genera Prevotellaceae_NK3B31 (p<0.01) and Chlamydia (p = 0.03) was lower in the MLAB group.

CONCLUSION

Overall, these results suggest that while MLAB supplementation does not directly improve piglet growth performance, it has the potential to improve immune function and promote a healthier gut microbiota in weaning piglets, which could ultimately reduce mortality rates.

Application of probiotic bacteria in ginsenoside bioconversion and enhancing its health-promoting benefits: a review

Ginseng (Panax) is a perennial herb with medicinal properties found in Asia and North America. Ginseng extracts contain several compounds, such as ginsenosides, which have therapeutic properties and have been extensively studied. Because of their deglycosylated nature, minor ginsenosides exhibit more potent bioactive properties than their parent ginsenosides. However, untreated ginseng extracts contain low levels of bioactive minor ginsenosides. Thus, converting major ginsenosides to minor ginsenosides using various methods, including microbial bioconversion, is required. Probiotic bacteria such as lactic acid bacteria and bifidobacteria are safe and excellent agents for bioconverting ginsenosides. Numerous studies have demonstrated the application of probiotic bacteria to produce minor ginsenosides; however, a comprehensive discussion focusing on using probiotics in ginsenoside bioconversion has been lacking. Therefore, this review investigates the application of probiotic bacteria to produce minor ginsenosides. Moreover, improving the health-promoting properties of ginseng with the help of probiotics is also reviewed.

A Narrative Review on the Impact of Probiotic Supplementation on Muscle Development, Metabolic Regulation, and Fiber Traits Related to Meat Quality in Broiler Chickens

Public concern over drug resistance has led to governmental regulations banning the use of antibiotics as growth promoters, stimulating interest in developing complementary strategies to maintain animal production, mitigate infections, and enhance muscle characteristics and quality parameters, especially in meat-producing animals. Probiotics are recognized as a potential strategy for improving growth, primarily by promoting intestinal homeostasis. These microorganisms are suggested to modulate gut microbiota, preserving their ecosystem and influencing secondary metabolite production, which can directly or indirectly regulate skeletal muscle metabolism by influencing the expression of key muscle-related genes and the activity of various signaling factors. Several studies have documented the potential benefits of various strains of Bacillus, Enterococcus, and members of the Lactobacillaceae family on muscle characteristics. These studies have shown that probiotics not only modulated myogenic factors but also influenced proteins and enzymes involved in signaling pathways related to carbon metabolism, inflammatory response, mitochondrial dynamics, and antioxidant activity. These effects have been associated with improvements in meat quality parameters and enhanced growth performance. This manuscript seeks to present a brief overview of the impact of probiotic supplementation on muscle health and the quality of meat in broiler chickens.

Absolute abundance calculation enhances the significance of microbiome data in antibiotic treatment studies

Background

The intestinal microbiota contributes to the colonization resistance of the gut towards bacterial pathogens. Antibiotic treatment often negatively affects the microbiome composition, rendering the host more susceptible for infections. However, a correct interpretation of such a perturbation requires quantitative microbiome profiling to reflect accurately the direction and magnitude of compositional changes within a microbiota. Standard 16S rRNA gene amplicon sequencing of microbiota samples offers compositional data in relative, but not absolute abundancies, and the presence of multiple copies of 16S rRNA genes in bacterial genomes introduces bias into compositional data. We explored whether improved sequencing data analysis influences the significance of the effect exerted by antibiotics on the faecal microbiota of young pigs using two veterinary antibiotics. Calculation of absolute abundances, either by flow cytometry-based bacterial cell counts or by spike-in of synthetic 16S rRNA genes, was employed and 16S rRNA gene copy numbers (GCN) were corrected.

Results

Cell number determination exhibited large interindividual variability in two pig studies, using either tylosin or tulathromycin. Following tylosin application, flow cytometry-based cell counting revealed decreased absolute abundances of five families and ten genera. These results were not detectable by standard 16S analysis based on relative abundances. Here, GCN correction additionally uncovered significant decreases of Lactobacillus and Faecalibacterium. In another experimental setting with tulathromycin treatment, bacterial abundance quantification by flow cytometry and by a spike-in method yielded similar results only on the phylum level. Even though the spike-in method identified the decrease of four genera, analysis by fluorescence-activated cell sorting (FACS) uncovered eight significantly reduced genera, such as Prevotella and Paraprevotella upon antibiotic treatment. In contrast, analysis of relative abundances only showed a decrease of Faecalibacterium and Rikenellaceae RC9 gut group and, thus, a much less detailed antibiotic effect.

Conclusion

Flow cytometry is a laborious method, but identified a higher number of significant microbiome changes in comparison to common compositional data analysis and even revealed to be superior to a spike-in method. Calculation of absolute abundances and GCN correction are valuable methods that should be standards in microbiome analyses in veterinary as well as human medicine.

FACdb: a comprehensive resource for genes, gut microbiota, and metabolites in farm animals

Farm animals, including livestock and poultry, play essential economic, social, and cultural roles and are indispensable in human welfare. Farm Animal Connectome database (FACdb) is a comprehensive resource that includes the association networks among gene expression, gut microbiota, and metabolites in farm animals. Although some databases present the relationship between gut microbes, metabolites, and gene expression, these databases are limited to human and mouse species, with limited data for farm animals. In this database, we calculate the associations and summarize the connections among gene expression, gut microbiota, and metabolites in farm animals using six correlation or distance calculation (including Pearson, Spearman, Cosine, Euclidean, Bray-Curtis, and Mahalanobis). FACdb contains over 55 million potential interactions of 73,571 genes, 11,046 gut microbiota, and 4,540 metabolites. It provides an easy-to-use interface for browsing and searching the association information. Additionally, FACdb offers interactive visualization tools to effectively investigate the relationship among the genes, gut microbiota, and metabolites in farm animals. Overall, FACdb is a valuable resource for understanding interactions among gut microbiota, metabolites, and gene expression. It contributes to the further utilization of microbes in animal products and welfare promotion. Compared to mice, pigs or other farm animals share more similarities with humans in molecular, cellular, and organ-level responses, indicating that our database may offer new insights into the relationship among gut microbiota, metabolites, and gene expression in humans.

Effects of organic acid-preserved cereal grains in sow diets during late gestation and lactation on the performance and faecal microbiota of sows and their offspring

BACKGROUND

Organic acids (OA) and maternal nutritional strategies have been demonstrated to promote piglet health and development. The objective of this study was to investigate the effects of incorporating OA-preserved cereal grains into sow diets during late gestation and lactation, aiming to reduce the metabolic demands of lactation while optimising offspring development and growth until slaughter. The experiment compared OA-preserved wheat and barley to conventionally dried grains, focusing on sow and offspring performance, as well as their faecal microbiota during lactation. Forty sows were blocked based on parity, body weight and back fat thickness on d 100 of gestation and assigned to one of two diets: a dried grain lactation diet and a preserved grain lactation diet. Sow faecal samples were collected at farrowing for the coefficient of apparent total tract digestibility (CATTD) of nutrients and microbial analysis. Offspring faecal samples were collected on d 10 postpartum and at weaning (d 26 postpartum) for microbial analysis.

RESULTS

Sow body weight, back fat changes, gestation and lactation length, total piglets born, wean-to-oestrus interval, and lactation efficiency were unaffected by sow diet (P > 0.05). However, sows offered the preserved grain diet exhibited improved CATTD of dry matter, nitrogen, gross energy, and neutral detergent fibre (P < 0.05). While no maternal effect was observed on offspring growth during lactation (P > 0.05), pigs from sows offered the preserved grain diet showed improved growth and feed efficiency from weaning until slaughter (d 168) compared to those from sows offered the dried grain diet (P < 0.05). The preserved grain diet also reduced the abundance of Proteobacteria in sow faeces at farrowing and in their offspring on d 10 postpartum, and improved piglet faecal scores throughout lactation (P = 0.05). At weaning, piglets from sows offered the preserved grain diet exhibited an increased abundance of Lactobacillus and reduced abundance of Alistipes in their faeces (P < 0.05).

CONCLUSION

OA-preserved grains enhanced the CATTD of nutrients in sows, promoted healthier piglet faecal scores during lactation, and improved offspring growth performance post-weaning, potentially linked to beneficial changes observed in the faecal microbiota of sows and their offspring during lactation.

Consequences of Domestication on Gut Microbiome: A Comparative Analysis Between Wild Boars and Domestic Pigs

The gut microbiota plays a vital role in the physiological functions and health of animals. Domestic pigs (Sus scrofa domesticus) and wild boars (Sus scrofa scrofa), which share a common ancestor, present a unique model for exploring the evolutionary changes in gut microbiota due to domestication. Comparing the gut microbiota of these two groups provides a unique opportunity to identify microorganisms that may have been lost or altered during domestication. This study employed 16S rRNA sequencing to compare the gut microbiota compositions of domestic pigs and wild boars, analyzing 69 fecal samples from both groups. Our results indicate significant differences in the taxonomic profiles of the gut microbiota between the two groups. Specifically, the genera Bifidobacterium and Lactobacillus, were found in higher abundance in wild boars. In contrast, domestic pigs exhibited a decreased variety of these potentially health-enhancing bacteria, likely due to factors such as simplified diets and antibiotic use. Functional gene analysis revealed that pathways related to carbohydrate metabolism, lipid metabolism, immune response, and environmental adaptability were more enriched in wild boars. These findings demonstrate significant differences in the gut microbiota composition between domestic pigs and wild boars, underscoring the impact of domestication on microbial diversity. Further research is necessary to explore the potential of transferring beneficial microbes from wild to domestic populations.

Applying recursive modelling to assess the role of the host genome and the gut microbiome on feed efficiency in pigs

The gut microbiome plays an important role in the performance and health of swine by providing essential nutrients and supporting the immune system. Recent studies have demonstrated that the gut microbiome can explain part of the variation observed in growth, health, and meat quality. Feed efficiency is crucial in swine production, as feed cost account for more than 60% of total production costs. This study aimed to assess the relationships between the host genome, gut microbiome, and feed efficiency in Iberian pigs raised under intensive conditions. The specific objectives were to assess the mediating effects of the gut microbiome on feed efficiency and to estimate the direct and total heritability of feed efficiency. The data set included the feed conversion ratio (FCR) and residual feed intake (RFI) from 587 Iberian pigs, as well as the 16S rRNA gut microbial abundance from 151 of those pigs raised in a nucleus of selection. We reparametrised variance components from standard bivariate mixed models into recursive models to disentangle the microbiome's mediating effect on feed efficiency. In our models, the host genome has direct effects on both the phenotype (G→P) and the gut microbiome (G→M). Additionally, there is an indirect effect of the host genome on the phenotype mediated by the microbiome (G→M→P). We identified a total of 14 taxa with relevant effects on FCR and 16 taxa with relevant effects on RFI. We categorised the gut microbiome into groups for potential practical application in pig farming. The gut microbes with relevant causal effects and low heritability can be manipulated through management interventions, while those microbes with relevant causal effects and moderate heritability can be targeted through selective breeding. Our findings indicate that incorporating microbiome data leads to a reduction in total heritability for both FCR and RFI. This study provides new insights into the link between the gut microbiome and feed efficiency, presenting practical methods to target microbes that can be influenced through selective breeding or management interventions.

Causal Association Between the Mucosal and Luminal Microbiotas from the Gastrointestinal Tract of Weaned Piglets Using Bayesian Network

The aim of this study was to investigate the microbiota composition and its potential interactions across seven gut locations (stomachs, jejuna, ilea, ceca, proximal colons, distal colons, and recta) in weaned pigs to identify key influencing microbiotas. To compare between microbiota compositions, 16S rRNA gene amplicon sequencing was performed. Six 70-day-old healthy crossbred (Duroc × Large White × Landrace) piglets were introduced as donors. A Bayesian network (BN) was used to examine the directional interactions among the microbiotas evaluated (seven mucosal and seven digesta microbiotas). Based on edge connectivity frequency, the microbiota in jejunal mucosa was the central hub node, influencing other microbiotas, especially the mucosal microbiotas of the ileum, cecum, distal colon, and rectum. The jejunal mucosa was dominated by Prevotella and lactobacilli, both recognized for their contributions to pig health. Among Prevotella, Prevotella copri and Prevotella sp. were predominant in jejunal mucosa (4.6% and 2.9%, respectively). Lactobacilli, including eight distinct species, were distributed throughout the gastrointestinal tract. Notably, Ligilactobacillus salivarius and Lactobacillus amylovorus, known as immune-enhancing bacteria, were abundant in jejunal mucosa (1.0% and 0.8%) and digestas (0.9% and 19.2%), respectively. The BN identified rectal mucosa and digestas as two terminal nodes, influenced by upstream microbiotas in the gastrointestinal tract. This finding supports the link between fecal microbiota and pig productivity, as the fecal microbiota, closely resembling the rectal microbiota, reflects the conditions of the microbiota throughout the gastrointestinal tract.

The Role of Nutrition Across Production Stages to Improve Sow Longevity

Modern hyperprolific sows are increasingly susceptible to health challenges. Their rapid growth rates predispose them to locomotor disorders, while high metabolic demands, reduced backfat thickness, and increased protein accretion heighten their vulnerability to heat stress and dystocia. Additionally, prolonged farrowing negatively affects the oxidative and inflammatory status of these females. Additionally, prevalent conditions such as gastric ulcers and cystitis raise ethical, welfare, and economic concerns. Despite the several studies related to sow nutrition, there are no studies which compile and extrapolate nutrition approaches from the rearing period and their impact on sows' health and longevity. Also, the aim of our review was to shed light on gaps that require further investigation. Controlling body condition scores is crucial for maximizing productivity in sows. During gestation, high-fiber diets help maintain optimal body condition and prevent constipation, particularly during the peripartum period. Antioxidants offer a range of beneficial effects during this critical phase. Additionally, probiotics and acidifiers can enhance gut health and lower the risk of genitourinary infections. On the day of farrowing, energy supplementation emerges as a promising strategy to reduce farrowing duration. Collectively, these strategies address major health challenges, enhancing welfare and promoting sow's longevity.

The potential probiotic role of Lacticaseibacillus rhamnosus on growth performance, gut health, and immune responses of weaned pigs

During the weaning period, piglets suffer from various challenges induced by changed trophic conditions, unstable immune systems, and exposure to unfamiliar environments accompanied by direct or indirect production losses. Supplementation of probiotics in a nursery diet has been considered an effective strategy that improves the growth rate and gut health of pigs. In swine production, lactic acid-producing bacteria (LAB), including Lactobacilli, are commonly used as prominent probiotics. Thus, the objective of this study was to evaluate the effects of dietary Lacticaseibacillus rhamnosus (LR), one of the Lactobacilli probiotics, on growth performance, frequency of diarrhea, nutrient digestibility, gut health, and immune responses of weaned pigs. A total of 48 pigs (6.51 ± 0.87kg; 28 d old) were allocated to 2 dietary treatments in a randomized complete block design (block: initial body weight). Dietary treatments were a basal nursery diet based on corn-soybean meal (CON) and CON + 0.02% LR (IDCC 3201; 2 × 109 CFU/g; Ildong Bioscience Co, Ltd, Seoul, Republic of Korea). The experiment was conducted for 4 wk. In this study, the LR group increased (P < 0.05) gain to feed ratio from d 1 to 7 compared with the CON group. Pigs fed LR had higher (P < 0.05) apparent total tract digestibility of dry matter, energy, and crude protein than those fed CON. The dietary LR decreased (P < 0.05) crypt depth in the duodenum and ileum compared with CON. The dietary LR upregulated ileal expression of the claudin-1 gene (P < 0.05) and tended to increase the claudin-2 gene (P = 0.089) while downregulated (P < 0.05) expression of tumor necrosis factor-α and interleukin-8 genes compared with CON. The LR group decreased (P < 0.05) platelet count on d 14 compared with the CON group. Furthermore, pigs fed LR had lower serum concentrations of the tumor necrosis factor-α on d 7 (P < 0.05) as well as interleukin-6 on d 7, 14, and 28 (P < 0.05) than those fed CON. This study suggests that the supplementation of 0.02% LR in the nursery diet can improve the growth performance and nutrient digestibility of weaned pigs by enhancing intestinal morphology, ileal gene expression of tight junction proteins and inflammatory cytokine, and systemic immune responses.

Dietary starch structure modulates nitrogen metabolism in laying hens via modifying glucose release rate

The objective of this study was to investigate the effects of starch structure (Amylopectin/Amylose, AP/AM) in a low-protein diet on production performance, nitrogen utilization efficiency, and cecal flora in laying hens. Four hundred eighty 45-wk-age Hy-Line Gray laying hens were randomly allocated to five dietary groups and subjected to a 12-wk feeding trial. The AP/AM ratios of the five experiment diets were 1.0, 1.5, 2.0, 3.0, and 4.0. The results indicated that compared to other groups, laying hens fed with AP/AM 4.0 diets showed significantly improved average egg weight and feed conversion ratio (P < 0.05). Furthermore, as the AP/AM ratio increased, there was a significant linear enhancement in intestinal amino acids apparent digestibility, apparent metabolizable energy, and villus area (P < 0.05). Compared to the high AP groups, high-AM diets significantly increased eggshell thickness, crude protein digestibility, and reduced energy supply from amino acid oxidation in ileum (P < 0.05). Additionally, moderate-AM diets enriched with short-chain fatty acid-producing bacteria in the cecum, such as Lactobacillus, Rikenellaceae_RC9_gut_group, and Christensenellaceae_R-7_group, which are associated with the promoting nitrogen utilization. These findings may offer useful information on optimizing starch structure for the design of food products and relevant therapies due to the potential effects on nutrient metabolism and gut homeostasis.

Effects of Dietary Net Energy Concentration on Reproductive Performance, Immune Function, Milk Composition, and Gut Microbiota in Primiparous Lactating Sows

This study aimed to determine the optimal dietary net energy concentration for the reproductive performance, immune function, milk composition, and gut microbiota of primiparous sows during lactation. Forty primiparous lactating sows (Landrace × Yorkshire) with similar body backfat thicknesses were randomly allocated into five treatment groups and fed diets with different dietary net energy concentrations of 10.05 MJ/kg, 10.47 MJ/kg, 10.89 MJ/kg, 11.30 MJ/kg, and 11.72 MJ/kg. The results showed that there were no differences in the performance of piglets, while there was a decrease in the daily feed intake of sows (p = 0.079, linear) as dietary net energy concentration increased. With the increasing dietary net energy concentration, the plasma insulin levels of sows increased (p < 0.01, linear), the plasma glucose levels tended to increase (p = 0.074, linear), and the blood urea nitrogen levels tended to decrease (p = 0.063, linear). Moreover, the plasma total superoxide dismutase activity of sows increased (p < 0.05, quadratic) and the plasma malondialdehyde content of sows decreased (p < 0.05, quadratic) by increasing the dietary net energy concentration. Interestingly, with the increase in dietary net energy concentration, the plasma immunoglobulin M content of sows increased, the milk immunoglobulin M, immunoglobulin G, immunoglobulin A and the percentage of milk fat increased (p < 0.05, linear), and the milk secretory immunoglobulin A content also increased (p < 0.05, linear and quadratic). The milk immunoglobulins and milk fat content of sows fed with net energy concentration of 11.72 MJ/kg were highest. Moreover, there were significant differences in the α-diversity, β-diversity, and relative abundance of gut microbiota in sows fed with different dietary net energy concentrations. At the phylum level, Spirochaetota and Bacteroidota in the gut microbiota of sows were mainly affected by increasing the dietary net energy concentration. Furthermore, the correlation analysis showed that milk immunoglobulin content had a significant negative correlation with the relative abundance of Bacteroidota, and plasma malondialdehyde content also had a significant negative correlation with the relative abundance of Spirochaetota. In summary, these results suggest that increasing the dietary net energy concentration to 11.72 MJ/kg can increase immunological substances in milk, improve milk quality, and alter the composition of gut microbiota in primiparous lactating sows.

Thermophile-fermented feed modulates the gut microbiota related to lactate metabolism in pigs

AIMS

Extracts of fermented feed obtained via fermentation of marine animal resources with thermophilic Bacillaceae bacteria increase the fecundity of livestock. The intestinal bacterial profiles in response to long-term administration of this extract to pigs were investigated.

METHODS AND RESULTS

Half of a swine farm was supplied with potable water containing an extract of fermented feed for more than 2 years, whereas the other half was supplied with potable water without the extract. Feces from 6-month-old pigs rearing in these two areas were collected. 16S rRNA gene sequencing and isolation of lactic acid bacteria revealed an increase in the D/L-lactate-producing bacterium, Lactobacillus amylovorus, and a decrease in several members of Clostridiales following administration of fermented feed. A lactate-utilizing bacterium, Megasphaera elsdenii, was more abundant in the feces of pigs in the fermented feed group. All representative isolates of M. elsdenii showed rapid utilization of D-lactate relative to L-lactate, and butyrate and valerate were the main products.

CONCLUSION

The probiotic effect of fermented feed is associated with the modulation of lactate metabolism in the digestive organs of pigs.

Branched Short-Chain Fatty Acid-Rich Fermented Protein Food Improves the Growth and Intestinal Health by Regulating Gut Microbiota and Metabolites in Young Pigs

The diet in early life is essential for the growth and intestinal health later in life. However, beneficial effects of a diet enriched in branched short-chain fatty acids (BSCFAs) for infants are ambiguous. This study aimed to develop a novel fermented protein food, enriched with BSCFAs and assess the effects of dry and wet ferment products on young pig development, nutrient absorption, intestinal barrier function, and gut microbiota and metabolites. A total of 18 young pigs were randomly assigned to three groups. The dry corn gluten-wheat bran mixture (DFCGW) and wet corn gluten-wheat bran mixture (WFCGW) were utilized as replacements for 10% soybean meal in the basal diet. Our results exhibited that the WFCGW diet significantly increased the growth performance of young pigs, enhanced the expression of tight junction proteins, and regulated associated cytokines expression in the colonic mucosa. Simultaneously, the WFCGW diet led to elevated levels of colonic isobutyric and isovaleric acid, as well as the activation of GPR41 and GPR109A. Furthermore, more potential probiotics including Lactobacillus, Megasphaera, and Lachnospiraceae_ND3007_group were enriched in the WFCGW group and positively associated with the beneficial metabolites such as 5-hydroxyindole-3-acetic acid. Differential metabolite KEGG pathway analysis suggested that WFCGW might exert gut health benefits by modulating tryptophan metabolism. In addition, the WFCGW diet significantly increased ghrelin concentrations in serum and hypothalamus and promoted the appetite of young pigs by activating hypothalamic NPY/AGRP neurons. This study extends the knowledge of BSCFAs and provides a reference for the fermented food application in the infant diet.

Breed-Driven Microbiome Heterogeneity Regulates Intestinal Stem Cell Proliferation via Lactobacillus-Lactate-GPR81 Signaling

Genetically lean and obese individuals have distinct intestinal microbiota and function. However, the underlying mechanisms of the microbiome heterogeneity and its regulation on epithelial function such as intestinal stem cell (ISC) fate remain unclear. Employing pigs of genetically distinct breeds (obese Meishan and lean Yorkshire), this study reveals transcriptome-wide variations in microbial ecology of the jejunum, characterized by enrichment of active Lactobacillus species, notably the predominant Lactobacillus amylovorus (L. amylovorus), and lactate metabolism network in obese breeds. The L. amylovorus-dominant heterogeneity is paralleled with epithelial functionality difference as reflected by highly expressed GPR81, more proliferative ISCs and activated Wnt/β-catenin signaling. Experiments using in-house developed porcine jejunal organoids prove that live L. amylovorus and its metabolite lactate promote intestinal organoid growth. Mechanistically, L. amylovorus and lactate activate Wnt/β-catenin signaling in a GPR81-dependent manner to promote ISC-mediated epithelial proliferation. However, heat-killed L. amylovorus fail to cause these changes. These findings uncover a previously underrepresented role of L. amylovorus in regulating jejunal stem cells via Lactobacillus-lactate-GPR81 axis, a key mechanism bridging breed-driven intestinal microbiome heterogeneity with ISC fate. Thus, results from this study provide new insights into the role of gut microbiome and stem cell interactions in maintaining intestinal homeostasis.

Impact of Lactobacillus- and Bifidobacterium-Based Direct-Fed Microbials on the Performance, Intestinal Morphology, and Fecal Bacterial Populations of Nursery Pigs

Weaning is a critical stage in the swine production cycle, as young pigs need to adjust to sudden and dramatic changes in their diet and environment. Among the various organ systems affected, the gastrointestinal tract is one of the more severely impacted during this transition. Traditionally, challenges at weaning have been managed by prophylactic use of antibiotics, which not only provides protection against diarrhea and other gut dysfunction but also has growth-promoting effects. With banning or major restrictions on the use of antibiotics for this purpose, various alternative products have been developed as potential replacements, including direct-fed microbials (DFMs) such as probiotics and postbiotics. As their efficiency needs to be improved, a continued effort to gain a deeper understanding of their mechanism of action is necessary. In this context, this report presents a study on the impact of a Lactobacillus-based probiotic (LPr) and a Bifidobacterium-based postbiotic (BPo) when added to the diet during the nursery phase. For animal performance, an effect was observed in the early stages (Day 0 to Day 10), as pigs fed diets supplemented with either DFMs were found to have higher average daily feed intake (ADFI) compared to pigs fed the control diet (p < 0.05). Histological analysis of intestinal morphology on D10 revealed that the ileum of supplemented pigs had a higher villus height/crypt depth ratio (p < 0.05) compared to controls, indicating a benefit of the DFMs for gut health. In an effort to further explore potential mechanisms of action, the effects of the DFMs on gut microbial composition were investigated using fecal microbial communities as a non-invasive representative approach. At the bacterial family level, Lactobacillaceae were found in higher abundance in pigs fed either LPr (D10; p < 0.05) or BPo (D47; p < 0.05). At the Operational Taxonomic Unit (OTU) level, which can be used as a proxy to assess species composition, Ssd-00950 and Ssd-01187 were found in higher abundance in DFM-supplemented pigs on D47 (p < 0.05). Using nucleotide sequence identity, these OTUs were predicted to be putative strains of Congobacterium massiliense and Absicoccus porci, respectively. In contrast, OTU Ssd-00039, which was predicted to be a strain of Streptococcus alactolyticus, was in lower abundance in BPo-supplemented pigs on D47 (p < 0.05). Together, these results indicate that the DFMs tested in this study can impact various aspects of gut function.

Alleviating Pentatrichomonas hominis-induced damage in IPEC-J2 cells: the beneficial influence of porcine-derived lactobacilli

Pentatrichomonas hominis is a common intestinal parasitic protozoan that causes abdominal pain and diarrhea, and poses a zoonotic risk. Probiotics, known for enhancing immunity and pathogen resistance, hold promise in combating parasitic infections. This study aimed to evaluate two porcine-derived probiotics, Lactobacillus reuteri LR1 and Lactobacillus plantarum LP1, against P. hominis infections in pigs. Taxonomic identity was confirmed through 16 S rRNA gene sequencing, with L. reuteri LR1 belonging to L. reuteri species and L. plantarum LP1 belonging to L. plantarum species. Both probiotics exhibited robust in vitro growth performance. Co-culturing intestinal porcine epithelial cell line (IPEC-J2) with these probiotics significantly improved cell viability compared with the control group. Pre-incubation probiotics significantly enhanced the mRNA expression of anti-oxidative response genes in IPEC-J2 cells compared with the PHGD group, with L. reuteri LR1 and L. plantarum LP1 significantly up-regulating CuZn-SOD、CAT and Mn-SOD genes expression (p < 0.05). The anti-oxidative stress effect of L. reuteri LR1 was significantly better than that of L. plantarum LP1 (p < 0.05). Furthermore, pre-incubation with the probiotics alleviated the P. hominis-induced inflammatory response. L. reuteri LR1 and L. plantarum LP1 significantly down-regulated IL-6、IL-8 and TNF-α gene expression(p < 0.05) compared with the PHGD group. The probiotics also mitigated P. hominis-induced apoptosis. L. reuteri LR1 and L. plantarum LP1 significantly down-regulated Caspase3 and Bax gene expression (p < 0.05), significantly up-regulated Bcl-2 gene expression (p < 0.05) compared with the PHGD group. Among them, L. plantarum LP1 showed better anti-apoptotic effect. These findings highlight the probiotics for mitigating P. hominis infections in pigs. Their ability to enhance anti-oxidative responses, alleviate inflammation, and inhibit apoptosis holds promise for therapeutic applications. Simultaneously, probiotics can actively contribute to inhibiting trichomonal infections, offering a novel approach for preventing and treating diseases such as P. hominis. Further in vivo studies are required to validate these results and explore their potential in animal and human health.

Isolation and Characterization of Lactic Acid Bacteria With Probiotic Attributes From Different Parts of the Gastrointestinal Tract of Free-living Wild Boars in Hungary

Lactic acid bacteria (LAB) in the microbiota play an important role in human and animal health and, when used as probiotics, can contribute to an increased growth performance in livestock management. Animals living in their native habitat can serve as natural sources of microorganisms, so isolation of LAB strains from wild boars could provide the opportunity to develop effective probiotics to improve production in swine industry. In this study, the probiotic potential of 56 LAB isolates, originated from the ileum, colon, caecum and faeces of 5 wild boars, were assessed in vitro in details. Their taxonomic identity at species level and their antibacterial activity against four representative strains of potentially pathogenic bacteria were determined. The ability to tolerate low pH and bile salt, antibiotic susceptibility, bile salt hydrolase activity and lack of hemolysis were tested. Draft genome sequences of ten Limosilactobacillus mucosae and three Leuconostoc suionicum strains were determined. Bioinformatic analysis excluded the presence of any known acquired antibiotic resistance genes. Three genes, encoding mesentericin B105 and two different bacteriocin-IIc class proteins, as well as two genes with possible involvement in mesentericin secretion (mesE) and transport (mesD) were identified in two L. suionicum strains. Lam29 protein, a component of an ABC transporter with proved function as mucin- and epithelial cell-adhesion factor, and a bile salt hydrolase gene were found in all ten L. mucosae genomes. Comprehensive reconsideration of all data helps to select candidate strains to assess their probiotic potential further in animal experiments.

Swine farm environmental microbiome: exploring microbial ecology and functionality across farms with high and low sanitary status

Introduction

Stringent regulations in pig farming, such as antibiotic control and the ban on certain additives and disinfectants, complicate disease control efforts. Despite the evolution of microbial communities inside the house environment, they maintain stability over the years, exhibiting characteristics specific to each type of production and, in some cases, unique to a particular company or farm production type. In addition, some infectious diseases are recurrent in specific farms, while other farms never present these diseases, suggesting a connection between the presence of these microorganisms in animals or their environment. Therefore, the aim of this study was to characterise environmental microbiomes of farms with high and low sanitary status, establishing the relationships between both, health status, environmental microbial ecology and its functionality.

Methods

For this purpose, 6 pig farms were environmentally sampled. Farms were affiliated with a production company that handle the majority of the pigs slaughtered in Spain. This study investigated the relationship among high health and low health status farms using high throughput 16S rRNA gene sequencing. In addition, to identify ecologically relevant functions and potential pathogens based on the 16S rRNA gene sequences obtained, functional Annotation with PROkaryotic TAXa (FAPROTAX) was performed.

Results and Discussion

This study reveals notable differences in microbial communities between farms with persistent health issues and those with good health outcomes, suggesting a need for protocols tailored to address specific challenges. The variation in microbial populations among farms underscores the need for specific and eco-friendly cleaning and disinfection protocols. These measures are key to enhancing the sustainability of livestock farming, ensuring safer products and boosting competitive edge in the market.

The possibly role of GnIH in stress and gut dysfunction in chicken

Stress is known to disrupt the intestinal barrier and induce intestinal dysfunction. A critical role for gonadotropin inhibitory hormone (GnIH) in stress has emerged. However, whether GnIH mediates stress-induced intestinal dysfunction remains unknown. The present study explored this question through in vivo and in vitro experiments in hens. Our in vivo experiments showed that continuous intraperitoneal injection of GnIH not only significantly increased the concentration of stress hormones in serum, but also significantly elevated the mRNA expression of glucocorticoid receptor (GR) in the duodenum and jejunum. Moreover, morphological and molecular analyses revealed that GnIH disrupted the physical and chemical barriers of the intestine and dramatically increased inflammatory factor levels in the intestine and serum of hens. Interestingly, the microbiomics results showed that GnIH altered the structure and composition of the gut flora in the cecum, revealing an increased abundance of harmful intestinal bacteria such as Desulfovibrionaceae. Similar results were found in in vitro studies in which the GnIH-induced intestinal mucosal barrier was disrupted, and inflammation increased in jejunal explants, although no significant difference was found in the expression of GR between the control and GnIH groups. Our results demonstrated that GnIH not only directly damaged intestinal barriers and elevated intestinal inflammation but also mediated stress and microflora imbalance-induced intestinal function disorder, suggesting that GnIH is a potential therapeutic target for gut dysfunction, stress-induced intestinal function disorder, and inflammatory bowel disease in animals and humans.

Defined Pig Microbiota Mixture as Promising Strategy against Salmonellosis in Gnotobiotic Piglets

Probiotics are a potential strategy for salmonellosis control. A defined pig microbiota (DPM) mixture of nine bacterial strains previously exhibited probiotic and anti-Salmonella properties in vitro. Therefore, we evaluated its gut colonization ability and protection effect against S. typhimurium LT2-induced infection in the gnotobiotic piglet model. The DPM mixture successfully colonized the piglet gut and was stable and safe until the end of the experiment. The colon was inhabited by about 9 log CFU g-1 with a significant representation of bifidobacteria and lactobacilli compared to ileal levels around 7-8 log CFU g-1. Spore-forming clostridia and bacilli seemed to inhabit the environment only temporarily. The bacterial consortium contributed to the colonization of the gut at an entire length. The amplicon profile analysis supported the cultivation trend with a considerable representation of lactobacilli with bacilli in the ileum and bifidobacteria with clostridia in the colon. Although there was no significant Salmonella-positive elimination, it seems that the administered bacteria conferred the protection of infected piglets because of the slowed delayed infection manifestation without translocations of Salmonella cells to the blood circulation. Due to its colonization stability and potential protective anti-Salmonella traits, the DPM mixture has promising potential in pig production applications. However, advanced immunological tests are needed.

Impact of Long-Term Supplementation with Probiotics on Gut Microbiota and Growth Performance in Post-Weaned Piglets

This study aimed to investigate effects of long-term probiotic supplementation on gut microbiota and growth performance in health weaned piglets. The non-probiotic group (N-PrB) was fed only a basal diet, while the probiotic group (PrB) was fed a basal diet + probiotic combination (E. faecium 1.6 × 108 CFU/g, B. subtilis 2.0 × 108 CFU/g, S. cerevisiae 3.0 × 108 CFU/g). The probiotics combination was provided to the PrB, mixing with the basal diet in 5 kg/ton. As a result, the PrB exhibited significantly improved weight gain compared to the N-PrB (p = 0.00991). In the gut microbiome analysis, the PrB exhibited a significant increasing tendency of α-diversity compared to those of the N-PrB (p < 0.01). In the bacterial relative abundance changes in bacteria comprising the gut microbiota, Ruminococcaceae (p = 0.00281) and Prevotella (p = 0.00687) tended to significantly increase in the PrB, but decreased in the N-PrB. The Eubaterium coprostanoligenes group exhibited an increasing tendency in both groups, but tended to increase more significantly in the PrB compared to the N-PrB (p = 0.00681). Muribaculaceae tended to significantly increase in the N-PrB, but decreased in the PrB (p = 0.002779). In this study, significant differences on the gut microbiome were found according to the probiotics supplementation in the weaned piglets and these gut microbiome changes appeared to improve the growth performance.

Bacillus amyloliquefaciens attenuates the intestinal permeability, oxidative stress and endoplasmic reticulum stress: transcriptome and microbiome analyses in weaned piglets

Endoplasmic reticulum (ER) stress is related to oxidative stress (OS) and leads to intestinal injury. Bacillus amyloliquefaciens SC06 (SC06) can regulate OS, but its roles in intestinal ER stress remains unclear. Using a 2 × 2 factorial design, 32 weaned piglets were treated by two SC06 levels (0 or 1 × 108 CFU/g), either with or without diquat (DQ) injection. We found that SC06 increased growth performance, decreased ileal permeability, OS and ER stress in DQ-treated piglets. Transcriptome showed that differentially expressed genes (DEGs) induced by DQ were enriched in NF-κB signaling pathway. DEGs between DQ- and SC06 + DQ-treated piglets were enriched in glutathione metabolism pathway. Ileal microbiome revealed that the SC06 + DQ treatment decreased Clostridium and increased Actinobacillus. Correlations were found between microbiota and ER stress genes. In conclusion, dietary SC06 supplementation increased the performance, decreased the permeability, OS and ER stress in weaned piglets by regulating ileal genes and microbiota.

Fatty acid-balanced oil improved nutrient digestibility, altered milk composition in lactating sows and fecal microbial composition in piglets

OBJECTIVE

This study aimed to investigate the effects of dietary supplementation of a fatty acid-balanced oil, instead of soybean oil, on reproductive performance, nutrient digestibility, blood indexes, milk composition in lactating sows, and fecal microbial composition in piglets.

METHODS

Twenty-four sows (Landrace×Yorkshire, mean parity 4.96) were randomly allotted to two treatments with twelve pens per treatment and one sow per pen based on their backfat thickness and parity. The experiment began on day 107 of gestation and continued until weaning on day 21 of lactation, lasting for 28 days. The control group (CG) was fed a basal diet supplemented with 2% soybean oil and the experimental group (EG) was fed the basal diet supplemented with 2% fatty acid-balanced oil.

RESULTS

The fatty acid-balanced oil supplementation increased (p<0.05) the apparent total tract digestibility of dry matter, crude protein, and gross energy in sows. The lower (p<0.05) serum high-density lipoprotein cholesterol and albumin levels of sows were observed in the EG on day 21 of lactation. Dietary supplementation with the fatty acid-balanced oil decreased the fat content, increased the immunoglobulin G level, and changed (p<0.05) some fatty acid content in milk. Moreover, the fatty acid-balanced oil supplementation changed (p<0.05) the fecal microbial composition of piglets, where the average relative abundance of Spirochaetota was decreased (p<0.05) by 0.55% at the phylum level, and the average relative abundance of some potentially pathogenic fecal microorganism was decreased (p<0.05) at the species level.

CONCLUSION

The fatty acid-balanced oil improved nutrient digestibility, changed the serum biochemical indices and milk composition of sows, and ameliorated the fecal microbial composition of piglets.

Change in the Gut Microbiota of Lactating Sows and Their Piglets by Inclusion of Dietary Spray-Dried Plasma in Sow Diets

This study aimed to investigate the effects of dietary spray-dried plasma (SDP) on the gut microbiota of lactating sows and their piglets. A total of 12 sows were randomly assigned to one of two dietary treatment groups in a completely randomized design. The treatments were a sow diet based on corn and soybean meal (CON), and a CON diet with an added 1% SDP. The sows were fed the dietary treatments from d 30 before farrowing to weaning (d 28). The fecal samples of three sows from each treatment and two of their randomly selected piglets were collected to verify their fecal microbiota. There were no differences in the alpha diversity and distinct clustering of the microbial communities in the sows and their piglets when SDP was added to the sow diets from late gestation to weaning. The fecal microbiota of the lactating sows and their piglets showed a higher relative abundance of the phylum Bacteroidota and genus Lactobacillus and Ruminococcus and showed a lower relative abundance of the phylum Bacillota and genus Bacteroides, Escherichia/Shigella, and Clostridium in the sows fed the SDP diet than those fed the CON diet. Overall, these results show that the addition of SDP to the sow diet during lactation altered the gut environment with positive microbial composition changes. These results were similar in the nursing piglets, suggesting that the control of the sow diets during lactation may contribute to the intestinal health and growth in piglets after weaning.

A first characterization of the microbiota-resilience link in swine

BACKGROUND

The gut microbiome plays a crucial role in understanding complex biological mechanisms, including host resilience to stressors. Investigating the microbiota-resilience link in animals and plants holds relevance in addressing challenges like adaptation of agricultural species to a warming environment. This study aims to characterize the microbiota-resilience connection in swine. As resilience is not directly observable, we estimated it using four distinct indicators based on daily feed consumption variability, assuming animals with greater intake variation may face challenges in maintaining stable physiological status. These indicators were analyzed both as linear and categorical variables. In our first set of analyses, we explored the microbiota-resilience link using PERMANOVA, α-diversity analysis, and discriminant analysis. Additionally, we quantified the ratio of estimated microbiota variance to total phenotypic variance (microbiability). Finally, we conducted a Partial Least Squares-Discriminant Analysis (PLS-DA) to assess the classification performance of the microbiota with indicators expressed in classes.

RESULTS

This study offers four key insights. Firstly, among all indicators, two effectively captured resilience. Secondly, our analyses revealed robust relationship between microbial composition and resilience in terms of both composition and richness. We found decreased α-diversity in less-resilient animals, while specific amplicon sequence variants (ASVs) and KEGG pathways associated with inflammatory responses were negatively linked to resilience. Thirdly, considering resilience indicators in classes, we observed significant differences in microbial composition primarily in animals with lower resilience. Lastly, our study indicates that gut microbial composition can serve as a reliable biomarker for distinguishing individuals with lower resilience.

CONCLUSION

Our comprehensive analyses have highlighted the host-microbiota and resilience connection, contributing valuable insights to the existing scientific knowledge. The practical implications of PLS-DA and microbiability results are noteworthy. PLS-DA suggests that host-microbiota interactions could be utilized as biomarkers for monitoring resilience. Furthermore, the microbiability findings show that leveraging host-microbiota insights may improve the identification of resilient animals, supporting their adaptive capacity in response to changing environmental conditions. These practical implications offer promising avenues for enhancing animal well-being and adaptation strategies in the context of environmental challenges faced by livestock populations. Video Abstract.

Leucine regulates lipid metabolism in adipose tissue through adipokine-mTOR-SIRT1 signaling pathway and bile acid-microbe axis in a finishing pig model

This study was conducted to explore the regulatory mechanism of leucine (Leu) on lipid metabolism of finishing pigs. Twenty-four Duroc × Landrace × Large cross pigs with an average body weight of 68.33 ± 0.97 kg were randomly allocated into 3 treatment groups with 8 replicates per group (1 pig per replicate). The dietary treatments were as follows: control group (CON), 0.25% Leu group and 0.50% Leu group. The experimental period was 42 d. The results showed as follows. (1) Compared with the CON, 0.25% and 0.50% Leu increased (P < 0.01) the average daily gain (ADG), while the average backfat thickness (ABT) and the ratio of feed intake to body weight gain (F:G ratio) were decreased (P < 0.05). (2) In the 0.25% Leu group, the relative mRNA expression levels of sterol regulatory element binding protein-1c (SREBP1c), recombinant fatty acid transport protein 1 (FATP1), chemerin and peroxisome proliferator-activated receptor γ (PPARγ) were decreased but the level of fatty acid binding protein 4 (FABP4) and fatty acid translocase (FAT/CD36) were increased in backfat tissue. In the 0.25% Leu group, the protein levels of p-Rictor, p-Raptor, p-eIF4E-binding protein 1 (p-4EBP1), p-silent mating type information regulator 2 homolog 1 (p-SIRT1) and acetylation ribosome s6 protein kinase 1 (Ac-S6K1) were increased (P < 0.05). (3) Compared to the CON, the diversity of gut microbiota in the 0.25% Leu group was increased. Principal component analysis showed that the relative abundance of Bacteroidetes, Lactobacillus and Desulfovibrio was higher in the 0.25% Leu group than the CON, but the relative abundance of Firmicutes, Treponema and Shigella was lower than in the CON (P < 0.05). (4) Four different metabolites were screened out from the serum of finishing pigs including allolithocholic acid (alloLCA), isolithocholic acid (isoLCA), ursodeoxycholic acid (UDCA) and hyodeoxycholic acid (HDCA), which correlate to various degrees with the above microorganisms. In conclusion, Leu could promote adipose tissue lipolysis of finishing pigs through the mTOR-SIRT1 signaling pathway, and S6K1 is acetylated at the same time, and the interaction between gut microbiota and bile acid metabolism is also involved.

Dietary Lactobacillus delbrueckii Affects Ileal Bacterial Composition and Circadian Rhythms in Pigs

Intestinal bacteria, synchronized with diet and feeding time, exhibit circadian rhythms and anticipate host gut function; however the effect of dietary probiotics on gut bacterial diurnal rhythms remains obscure. In this study, bacteria were sequenced at 6 Zeitgeber times (ZT) from a pig model of ileal T-shaped fistula to test ileal bacterial composition and circadian rhythms after Lactobacillus delbrueckii administration. The results showed that dietary L. delbrueckii enhanced ileal bacterial α-diversity at Zeitgeber time (ZT) 16, evidenced by an increased Simpson index compared with control pigs. At the phylum level, Firmicutes was identified as the largest phyla represented in pigs, but dietary L. delbrueckii only increased the abundance of Tenericutes at ZT16. At the genus level, 11/100 genera (i.e., Lactobacillus, Enterococcus, Leptotrichia, Pediococcus, Bifidobacte, Cellulosilyticum, Desulfomicrobium, Sharpea, Eubacterium, Propionivibrio, and Aerococcus) were markedly differentiated in L. delbrueckii-fed pigs and the effect was rhythmicity-dependent. Meanwhile, dietary L. delbrueckii affected six pathways of bacterial functions, such as membrane transport, metabolism of cofactors and vitamins, cell motility, the endocrine system, signaling molecules and interaction, and the nervous system. Cosinor analysis was conducted to test bacterial circadian rhythm in pigs, while no significant circadian rhythm in bacterial α-diversity and phyla composition was observed. Lactobacillus, Terrisporobacter, and Weissella exhibited significant rhythmic fluctuation in the control pigs, which was disturbed by probiotic exposure. In addition, dietary L. delbrueckii affected circadian rhythms in ileal Romboutsia, Erysipelatoclostridium, Cellulosilyticum, and Eubacterium abundances. Dietary L. delbrueckii affected both ileal bacterial composition and circadian rhythms, which might further regulate gut function and host metabolism in pigs.

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.

Gut microbiota reflect adaptation of cave-dwelling tadpoles to resource scarcity

Gut microbiota are significant to the host's nutrition and provide a flexible way for the host to adapt to extreme environments. However, whether gut microbiota help the host to colonize caves, a resource-limited environment, remains unknown. The nonobligate cave frog Oreolalax rhodostigmatus completes its metamorphosis within caves for 3-5 years before foraging outside. Their tadpoles are occasionally removed from the caves by floods and utilize outside resources, providing a contrast to the cave-dwelling population. For both cave and outside tadpoles, the development-related reduction in their growth rate and gut length during prometamorphosis coincided with a shift in their gut microbiota, which was characterized by decreased Lactobacillus and Cellulosilyticum and Proteocatella in the cave and outside individuals, respectively. The proportion of these three genera was significantly higher in the gut microbiota of cave-dwelling individuals compared with those outside. The cave-dwellers' gut microbiota harbored more abundant fibrolytic, glycolytic, and fermentative enzymes and yielded more short-chain fatty acids, potentially benefitting the host's nutrition. Experimentally depriving the animals of food resulted in gut atrophy for the individuals collected outside the cave, but not for those from inside the cave. Imitating food scarcity reproduced some major microbial features (e.g. abundant Proteocatella and fermentative genes) of the field-collected cave individuals, indicating an association between the cave-associated gut microbiota and resource scarcity. Overall, the gut microbiota may reflect the adaptation of O. rhodostigmatus tadpoles to resource-limited environments. This extends our understanding of the role of gut microbiota in the adaptation of animals to extreme environments.

Lactation-related dynamics of bacterial and fungal microbiomes in feces of sows and gut colonization in suckling and newly weaned piglets

Changes in the gut microbial composition of the sow during lactation may influence the gut microbial colonization in their offspring, for which less information was available in the literature. This study aimed to assess: 1) the changes that occur in the bacterial and fungal communities in sow feces during the 28-d lactation period as well as in gastric and cecal digesta of piglets until one week after weaning, and 2) bacterial and fungal taxa in cecal digesta of the piglets postweaning that associate with fecal consistency. Aside from sow milk, piglets had access to creep feed from day of life (DoL) 3. Fecal samples from sows for microbial analysis were collected (n = 20) on days postpartum (DPP) 1, 6, 13, 20, and 27, as well as from weaned piglets for fecal scoring on DoL 30 and 34. Gastric and cecal digesta of piglets was collected on DoL3, 7, 14, 21, 28, 31, and 35 (n = 5/sex/DoL). Progressing lactation affected bacterial and fungal communities in sow feces, including 10.3- and 3.0-fold increases in the relative abundances of Lactobacillus from DPP1 to 6 and Kazachstania from DPP1 to 13, respectively (P < 0.001). Although time- and gut-site-related differences existed, bacterial and fungal taxa found in sow feces were also present in gastric and cecal digesta of piglets, which supports their role in gut colonization in neonatal piglets. In piglets, bacterial and fungal alpha-diversities showed certain fluctuations during the suckling period, whereby weaning affected the fungal than bacterial diversity at both gut sites (P < 0.05). At both gut sites, Lactobacillus largely increased from DoL3 to 7 and remained a dominating taxon until DoL35 (P < 0.05). Postweaning, plant-glycan fermenters (e.g., Prevotella-9) seemed to replace milk-glycan fermenting Fusobacterium and Bacteroides (P < 0.05). In gastric and cecal digesta, Kazachstania, Tausonia, Candida, and Blumeria were dominating fungi from DoL3 to 35, with Kazachstania becoming even more dominant postweaning (P < 0.001). Fecal consistency was softer on DoL34 than 30 (P < 0.05). Correlation analysis identified that softer feces were linked to the relative abundances of plant-glycan and proteolytic bacterial taxa including pathobionts (e.g., Clostridium sensu stricto) in the cecum on DoL34. However, the potential association between cecal mold and plant-pathogenic fungi Talaromyces, Mrakia, and Blumeria and softer feces are worth investigating in the future in relation to (gut) health of piglets.

Dietary supplementation with dihydroartemisinin improves intestinal barrier function in weaned piglets with intrauterine growth retardation by modulating the gut microbiota

The aim of this study was to investigate whether dietary dihydroartemisinin (DHA) supplementation could improve intestinal barrier function and microbiota composition in intrauterine growth restriction (IUGR) weaned piglets. Twelve normal birth weight (NBW) piglets and 24 IUGR piglets at 21 d of age were divided into three groups, which were fed a basal diet (NBW-CON and IUCR-CON groups) and an 80 mg/kg DHA diet (IUGR-DHA group). At 49 d of age, eight piglets of each group with similar body weights within groups were slaughtered, and serum and small intestine samples were collected. The results showed that IUGR piglets reduced growth performance, impaired the markers of intestinal permeability, induced intestinal inflammation, decreased intestinal immunity, and disturbed the intestinal microflora. Dietary DHA supplementation increased average daily gain, average daily feed intake, and body weight at 49 d of age in IUGR-weaned piglets (P < 0.05). DHA treatment decreased serum diamine oxidase activity and increased the numbers of intestinal goblet cells and intraepithelial lymphocytes, concentrations of jejunal mucin-2 and ileal trefoil factor 3, and intestinal secretory immunoglobin A and immunoglobin G (IgG) concentrations of IUGR piglets (P < 0.05). Diet supplemented with DHA also upregulated mRNA abundances of jejunal IgG, the cluster of differentiation 8 (CD8), major histocompatibility complex-I (MHC-I), and interleukin 6 (IL-6) and ileal IgG, Fc receptor for IgG (FcRn), cluster of differentiation 8 (CD4), CD8, MHC-I, IL-6 and tumor necrosis factor α (TNF-α), and enhanced mRNA abundance and protein expression of intestinal occludin and ileal claudin-1 in IUGR piglets (P < 0.05). In addition, DHA supplementation in the diet improved the microbial diversity of the small intestine of IUGR piglets and significantly increased the relative abundance of Actinobacteriota, Streptococcus, Blautia and Streptococcus in the jejunum, and Clostridium sensu_ stricto_in the ileum (P < 0.05). The intestinal microbiota was correlated with the mRNA abundance of tight junction proteins and inflammatory response-related genes. These data suggested that DHA could improve the markers of intestinal barrier function in IUGR-weaned piglets by modulating gut microbiota. DHA may be a novel nutritional candidate for preventing intestinal dysfunction in IUGR pigs.

Growth Performance, Metabolomics, and Microbiome Responses of Weaned Pigs Fed Diets Containing Growth-Promoting Antibiotics and Various Feed Additives

The objective of this study was to determine the potential biological mechanisms of improved growth performance associated with potential changes in the metabolic profiles and intestinal microbiome composition of weaned pigs fed various feed additives. Three separate 42 day experiments were conducted to evaluate the following dietary treatments: chlortetracycline and sulfamethazine (PC), herbal blends, turmeric, garlic, bitter orange extract, sweet orange extract, volatile and semi-volatile milk-derived substances, yeast nucleotide, and cell wall products, compared with feeding a non-supplemented diet (NC). In all three experiments, only pigs fed PC had improved (p < 0.05) ADG and ADFI compared with pigs fed NC. No differences in metabolome and microbiome responses were observed between feed additive treatments and NC. None of the feed additives affected alpha or beta microbiome diversity in the ileum and cecum, but the abundance of specific bacterial taxa was affected by some dietary treatments. Except for feeding antibiotics, none of the other feed additives were effective in improving growth performance or significantly altering the metabolomic profiles, but some additives (e.g., herbal blends and garlic) increased (p < 0.05) the relative abundance of potentially protective bacterial genera that may be beneficial during disease challenge in weaned pigs.

BDE-209-induced genotoxicity, intestinal damage and intestinal microbiota dysbiosis in zebrafish (Danio Rerio)

The environmental presence of polybrominated diphenyl ethers (PBDEs) is ubiquitous due to their wide use as brominated flame retardants in industrial products. As a common congener of PBDEs, decabromodiphenyl ether (BDE-209) can pose a health risk to animals as well as humans. However, to date, few studies have explored BDE-209's toxic effects on the intestinal tract, and its relevant mechanism of toxicity has not been elucidated. In this study, adult male zebrafish were exposed to BDE-209 at 6 μg/L, 60 μg/L and 600 μg/L for 28 days, and intestinal tissue and microbial samples were collected for analysis to reveal the underlying toxic mechanisms. Transcriptome sequencing results demonstrated a dose-dependent pattern of substantial gene differential expression in the group exposed to BDE-209, and the differentially expressed genes were mainly concentrated in pathways related to protein synthesis and processing, redox reaction, and steroid and lipid metabolism. In addition, BDE-209 exposure caused damage to intestinal structure and barrier function, and promoted intestinal oxidative stress, inflammatory response, apoptosis and steroid and lipid metabolism disorders. Mechanistically, BDE-209 induced intestinal inflammation by increasing the levels of TNF-α and IL-1β and activating the NFκB signaling pathway, and might induce apoptosis through the p53-Bax/Bcl2-Caspase3 pathway. BDE-209 also significantly inhibited the gene expression of rate-limiting enzymes such as Sqle and 3βhsd (p < 0.05) to inhibit cholesterol synthesis. In addition, BDE-209 induced lipid metabolism disorders through the mTOR/PPARγ/RXRα pathway. 16S rRNA sequencing results showed that BDE-209 stress reduced the richness and diversity of intestinal microbiota, and reduced the abundance of probiotics (e.g., Bifidobacterium and Faecalibacterium). Overall, the results of this study help to clarify the intestinal response mechanism of BDE-209 exposure, and provide a basis for evaluating the health risks of BDE-209 in animals.

Comparative evaluation of the fecal microbiota of adult hybrid pigs and Tibetan pigs, and dynamic changes in the fecal microbiota of hybrid pigs

The breed of pig can affect the diversity and composition of fecal microbiota, but there is a lack of research on the fecal microbiota of hybrid pigs. In this study, feces samples from Chuanxiang black pigs (a hybrid of Tibetan and Duroc pigs) aged 3 days (n = 24), 70 days (n = 31), 10 months (n = 13) and 2 years (n = 30) and Tibetan pigs aged 10 months (n = 14) and 2 years (n = 15) were collected and sequenced by 16S rRNA gene sequencing technology. We also measured the weight of all the tested pigs and found that the 10-month-old and two-year-old Chuanxiang black pigs weighed about three times the weight of Tibetan pigs of the same age. After comparing the genus-level microbiota composition of Tibetan pigs and Chuanxiang black pigs at 10 months and two years of age, we found that Treponema and Streptococcus were the two most abundant bacteria in Chuanxiang black pigs, while Treponema and Chirstensenellaceae_R.7_group were the two most abundant bacteria in Tibetan pigs. Prediction of microbial community function in adult Chuanxiang black pigs and Tibetan pigs showed changes in nutrient absorption, disease resistance, and coarse feeding tolerance. In addition, we also studied the changes in fecal microbiota in Chuanxiang black pigs at 3 days, 70 days, 10 months, and 2 years of age. We found that the ecologically dominant bacteria in fecal microbiota of Chuanxiang black pigs changed across developmental stages. For example, the highest relative abundance of 70-day-old Chuanxiang black pigs at the genus level was Prevotella. We identified specific microbiota with high abundance at different ages for Chuanxiang black pigs, and revealed that the potential functions of these specific microbiota were related to the dominant phenotype such as fast growth rate and strong disease resistance. Our findings help to expand the understanding of the fecal microbiota of hybrid pigs and provide a reference for future breeding and management of hybrid pigs.

Euglena gracilis β-Glucans (1,3): Enriching Colostrum of Sow for Enhanced Piglet Immunity

The effects of supplementing the diet of sows with βG-(1,3) derived from Euglena gracilis algae were assessed regarding quality and amount of colostrum as well as performance of piglets. A total of 120 sows (first (nulliparous) to sixth parity (multiparous)) from D85 of gestation until weaning were divided into two groups: the control diet group (n = 60) and the βG-(1,3) diet group (n = 60). Sows receiving βG-(1,3) exhibited an average increase of 870 g (24.9%) in colostrum production, leading to a 25.17% higher intake of colostrum by piglets. Furthermore, piglets in the βG-(1,3) group showed significantly superior weight gain of 34 g (50%) compared to the control group 18 h after birth (p < 0.05). Sows fed with βG-(1,3) produced colostrum with significantly higher concentrations of IgG (5.914 mg/mL, 16.16%) and IgM (0.378 mg/mL, 16.29%) than the control group (p < 0.05). Similarly, serum concentrations of IgG (13.86 mg/mL, 51.25%), IgA (17.16 mg/mL, 120.19%), and IgM (13.23 mg/mL, 144.78%) were significantly higher in sows fed with βG-(1,3) than in the control group (p < 0.05). Supplementing sows with βG-(1,3) derived from the Euglena gracilis algae resulted in increased colostrum production and consumption, along with greater weight gain in piglets during the first 18 h after birth. Additionally, both the colostrum produced by the sows and the blood serum of the piglets exhibited higher concentrations of immunoglobulins.

Research Progress of Biological Feed in Beef Cattle

Biological feed is a feed product developed through bioengineering technologies such as fermentation engineering, enzyme engineering, protein engineering, and genetic engineering. It possesses functional characteristics of high nutritional value and good palatability that can improve feed utilization, replace antibiotics, enhance the health level of livestock and poultry, improve the quality of livestock products, and promote a better breeding environment. A comprehensive review is provided on the types of biological feed, their mechanism of action, fermenting strains, fermenting raw material resources, and their current status in animal production to facilitate in-depth research and development of applications.

Comparison of the gut microbiota and metabolites between Diannan small ear pigs and Diqing Tibetan pigs

Objective

Host genetics and environment participate in the shaping of gut microbiota. Diannan small ear pigs and Diqing Tibetan pigs are excellent native pig breeds in China and live in different environments. However, the gut microbiota of Diannan small ear pigs and Diqing Tibetan pigs were still rarely understood. Therefore, this study aimed to analyze the composition characteristics of gut microbiota and metabolites in Diannan small ear pigs and Diqing Tibetan pigs.

Methods

Fresh feces of 6 pigs were randomly collected from 20 4-month-old Diannan small ear pigs (DA group) and 20 4-month-old Diqing Tibetan pigs (TA group) for high-throughput 16S rRNA sequencing and liquid chromatography-mass spectrometry (LC-MS) non-targeted metabolome analysis.

Results

The results revealed that Firmicutes and Bacteroidetes were the dominant phyla in the two groups. Chao1 and ACE indices differed substantially between DA and TA groups. Compared with the DA group, the relative abundance of Prevotellaceae, and Ruminococcus was significantly enriched in the TA group, while the relative abundance of Lachnospiraceae, Actinomyces, and Butyricicoccus was significantly reduced. Cholecalciferol, 5-dehydroepisterol, stigmasterol, adrenic acid, and docosahexaenoic acid were significantly enriched in DA group, which was involved in the steroid biosynthesis and biosynthesis of unsaturated fatty acids. 3-phenylpropanoic acid, L-tyrosine, phedrine, rhizoctin B, and rhizoctin D were significantly enriched in TA group, which was involved in the phenylalanine metabolism and phosphonate and phosphinate metabolism.

Conclusion

We found that significant differences in gut microbiota composition and metabolite between Diannan small ear pigs and Diqing Tibetan pigs, which provide a theoretical basis for exploring the relationship between gut microbiota and pig breeds.

Effect of Red-Beetroot-Supplemented Diet on Gut Microbiota Composition and Metabolite Profile of Weaned Pigs-A Pilot Study

Red beetroot is a well-recognized and established source of bioactive compounds (e.g., betalains and polyphenols) with anti-inflammatory and antimicrobial properties. It is proposed as a potential alternative to zinc oxide with a focus on gut microbiota modulation and metabolite production. In this study, weaned pigs aged 28 days were fed either a control diet, a diet supplemented with zinc oxide (3000 mg/kg), or 2% and 4% pulverized whole red beetroot (CON, ZNO, RB2, and RB4; respectively) for 14 days. After pigs were euthanized, blood and digesta samples were collected for microbial composition and metabolite analyses. The results showed that the diet supplemented with red beetroot at 2% improved the gut microbial richness relative to other diets but marginally influenced the cecal microbial diversity compared to a zinc-oxide-supplemented diet. A further increase in red beetroot levels (4%-RB4) led to loss in cecal diversity and decreased short chain fatty acids and secondary bile acid concentrations. Also, an increased Proteobacteria abundance, presumably due to increased lactate/lactic-acid-producing bacteria was observed. In summary, red beetroot contains several components conceived to improve the gut microbiota and metabolite output of weaned pigs. Future studies investigating individual components of red beetroot will better elucidate their contributions to gut microbiota modulation and pig health.

The gut microbiome and resistome of conventionally vs. pasture-raised pigs

Conventional swine production typically houses pigs indoors and in large groups, whereas pasture-raised pigs are reared outdoors at lower stocking densities. Antimicrobial use also differs, with conventionally raised pigs often being exposed to antimicrobials directly or indirectly to control and prevent infectious disease. However, antimicrobial use can be associated with the development and persistence of antimicrobial resistance. In this study, we used shotgun metagenomic sequencing to compare the gut microbiomes and resistomes of pigs raised indoors on a conventional farm with those raised outdoors on pasture. The microbial compositions as well as the resistomes of both groups of pigs were significantly different from each other. Bacterial species such as Intestinibaculum porci, Pseudoscardovia radai and Sharpea azabuensis were relatively more abundant in the gut microbiomes of pasture-raised pigs and Hallella faecis and Limosilactobacillus reuteri in the conventionally raised swine. The abundance of antimicrobial resistance genes (ARGs) was significantly higher in the conventionally raised pigs for nearly all antimicrobial classes, including aminoglycosides, beta-lactams, macrolides-lincosamides-streptogramin B, and tetracyclines. Functionally, the gut microbiomes of the two group of pigs also differed significantly based on their carbohydrate-active enzyme (CAZyme) profiles, with certain CAZyme families associated with host mucin degradation enriched in the conventional pig microbiomes. We also recovered 1043 dereplicated strain-level metagenome-assembled genomes (≥90 % completeness and <5 % contamination) to provide taxonomic context for specific ARGs and metabolic functions. Overall, the study provides insights into the differences between the gut microbiomes and resistomes of pigs raised under two very different production systems.

Probiotics and Postbiotics as an Alternative to Antibiotics: An Emphasis on Pigs

Probiotics are being used as feed/food supplements as an alternative to antibiotics. It has been demonstrated that probiotics provide several health benefits, including preventing diarrhea, irritable bowel syndrome, and immunomodulation. Alongside probiotic bacteria-fermented foods, the different structural components, such as lipoteichoic acids, teichoic acids, peptidoglycans, and surface-layer proteins, offer several advantages. Probiotics can produce different antimicrobial components, enzymes, peptides, vitamins, and exopolysaccharides. Besides live probiotics, there has been growing interest in consuming inactivated probiotics in farm animals, including pigs. Several reports have shown that live and killed probiotics can boost immunity, modulate intestinal microbiota, improve feed efficiency and growth performance, and decrease the incidence of diarrhea, positioning them as an interesting strategy as a potential feed supplement for pigs. Therefore, effective selection and approach to the use of probiotics might provide essential features of using probiotics as an important functional feed for pigs. This review aimed to systematically investigate the potential effects of lactic acid bacteria in their live and inactivated forms on pigs.

Cefquinome shows a higher impact on the pig gut microbiome and resistome compared to ceftiofur

Cephalosporins are licensed for treatment of severe bacterial infections in different species. However, the effect of these antimicrobials on the fecal microbiome and potential spread of resistance-associated genes causes great concern. This highlights the need to understand the impact of cephalosporins on the porcine fecal microbiome and resistome. A combination of long-read 16S rRNA gene and shotgun metagenomic sequencing was applied to investigate the effect of conventional treatment with either ceftiofur (3 mg.kg^-1 intramuscular, 3 consecutive days) or cefquinome (2 mg.kg^-1 intramuscular, 5 consecutive days) on the porcine microbiome and resistome. Fecal samples were collected from 17 pigs (6 ceftiofur treated, 6 cefquinome treated, 5 control pigs) at four different timepoints. Treatment with ceftiofur resulted in an increase in Proteobacteria members on microbiome level, while on resistome level selection in TetQ containing Bacteroides, CfxA6 containing Prevotella and bla_TEM-1 containing Escherichia coli was observed. Cefquinome treatment resulted in a decline in overall species richness (α-diversity) and increase in Proteobacteria members. On genus level, administration of cefquinome significantly affected more genera than ceftiofur (18 vs 8). On resistome level, cefquinome resulted in a significant increase of six antimicrobial resistance genes, with no clear correlation with certain genera. For both antimicrobials, the resistome levels returned back to the control levels 21 days post-treatment. Overall, our study provides novel insights on the effect of specific cephalosporins on the porcine gut microbiome and resistome after conventional intramuscular treatment. These results might contribute to better tailoring of the most ideal treatment strategy for some bacterial infections.

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.

Gut Microbiota and Behavioural Issues in Production, Performance, and Companion Animals: A Systematic Review

The literature has identified poor nutrition as the leading factor in the manifestation of many behavioural issues in animals, including aggression, hyperalertness, and stereotypies. Literature focused on all species of interest consistently reported that although there were no significant differences in the richness of specific bacterial taxa in the microbiota of individual subjects with abnormal behaviour (termed alpha diversity), there was variability in species diversity between these subjects compared to controls (termed beta diversity). As seen in humans with mental disorders, animals exhibiting abnormal behaviour often have an enrichment of pro-inflammatory and lactic acid-producing bacteria and a reduction in butyrate-producing bacteria. It is evident from the literature that an association exists between gut microbiota diversity (and by extension, the concurrent production of microbial metabolites) and abnormal behavioural phenotypes across various species, including pigs, dogs, and horses. Similar microbiota population changes are also evident in human mental health patients. However, there are insufficient data to identify this association as a cause or effect. This review provides testable hypotheses for future research to establish causal relationships between gut microbiota and behavioural issues in animals, offering promising potential for the development of novel therapeutic and/or preventative interventions aimed at restoring a healthy gut-brain-immune axis to mitigate behavioural issues and, in turn, improve health, performance, and production in animals.

Full-length 16S rRNA gene sequencing and machine learning reveal the bacterial composition of inhalable particles from two different breeding stages in a piggery

Bacterial loading aggravates the harm of particulate matter (PM) to public health and ecological systems, especially in operations of concentrated animal production. This study aimed to explore the characteristics and influencing factors of bacterial components of inhalable particles at a piggery. The morphology and elemental composition of coarse particles (PM₁₀, aerodynamic diameter ≤ 10 µm) and fine particles (PM_2.5, aerodynamic diameter ≤ 2.5 µm) were analyzed. Full-length 16 S rRNA sequencing technology was used to identify bacterial components according to breeding stage, particle size, and diurnal rhythm. Machine learning (ML) algorithms were used to further explore the relationship between bacteria and the environment. The results showed that the morphology of particles in the piggery differed, and the morphologies of the suspected bacterial components were elliptical deposited particles. Full-length 16 S rRNA indicated that most of the airborne bacteria in the fattening and gestation houses were bacilli. The analysis of beta diversity and difference between samples showed that the relative abundance of some bacteria in PM_2.5 was significantly higher than that in PM₁₀ at the same pig house (P < 0.01). There were significant differences in the bacterial composition of inhalable particles between the fattening and gestation houses (P < 0.01). The aggregated boosted tree (ABT) model showed that PM_2.5 had a great influence on airborne bacteria among air pollutants. Fast expectation-maximization microbial source tracking (FEAST) showed that feces was a major potential source of airborne bacteria in pig houses (contribution 52.64-80.58 %). These results will provide a scientific basis for exploring the potential risks of airborne bacteria in a piggery to human and animal health.