Meta-analysis To Define a Core Microbiota in the Swine Gut

Assessing the relationship between the gut microbiota and growth traits in Chinese indigenous pig breeds

BACKGROUND

Gut microbiota plays crucial roles in host metabolism, diseases and development. It has also been reported to be associated with growth performance in pigs. However, the bacterial species influencing pig growth performance have not been isolated, and the mechanisms remain unclear.

RESULTS

In this study, we collected 500 gut microbial samples from two Chinese indigenous pig breeds, including 244 fecal samples from Bamaxiang (BMX) pigs and 256 cecum content samples from Erhualian (EHL) pigs, to investigate the relationship between gut microbiota and pig growth traits. Bacterial compositions were determined by 16 S rRNA gene sequencing, and association analysis was performed using a two-part model. We found that the Firmicutes-to-Bacteroidota ratio in fecal samples from BMX pigs was negatively associated with average daily gain (P = 0.0085). Amplicon sequence variants (ASVs) belonging to Prevotella and three ASVs annotated to Oscillospiraceae were negatively associated with pig growth traits, while ASVs annotated to Muribaculaceae and Rikenellaceae showed positive correlations with growth traits in BMX fecal samples. In cecum content samples from EHL pigs, ASVs belonging to Prevotella, Lactobacillus delbrueckii, and Lachnospiraceae were negatively associated with growth performance, whereas one ASV belonging to Rikenellaceae demonstrated a positive association. Predicted functional capacity analysis revealed that metabolic pathways related to the digestive system, glycan biosynthesis and metabolism, signaling molecules and interactions, and xenobiotics biodegradation and metabolism were positively associated with pig growth traits. Conversely, the excretory system pathway showed a negative correlation. These pathways were found to correlate with growth trait-associated bacterial ASVs, suggesting that alterations in gut bacterial composition led to functional capacity shifts in the gut microbiome, subsequently affecting porcine growth.

CONCLUSIONS

Our results gave significant insights about the effect of gut microbiota on pig growth and provided important evidence to support further isolation of bacterial taxa that influence pig growth for elucidating their mechanisms.

Unraveling the microbial diversity of bovine liver abscesses: isolation, identification, and genomic characterization of the Bacteroides found in hepatic lesions

Liver abscesses in cattle reduce animal performance, increase the environmental footprint of beef production, and cause significant economic losses. The low pH of the rumen resulting from the consumption of high grain diets damages the rumen epithelium and facilitates the translocation of opportunistic pathogens from the gastrointestinal tract into the bloodstream where they can colonize the liver, causing infection. Recently, 16s rRNA sequencing has revealed that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides. Due to the inability to reliably classify amplicon sequences beyond the genus level, the identity of these microbes remains unknown. We have employed a combination of culture-independent and culture-based methods to isolate and identify the Bacteroides associated with liver abscesses in cattle. Shotgun metagenomic sequencing and assembly of metagenome-assembled genomes generated four high-quality genomes, two of which were putatively identified as Bacteroides. These microbes were subsequently isolated from the purulent material of liver abscesses. Whole-genome sequencing conclusively identified these isolates as Bacteroides pyogenes and a previously unknown species of Bacteroides, revealing distinct differences from Bacteroides typically found in the gut. Carbohydrate utilization assays revealed that both organisms metabolize glycogen and glycosaminoglycans found in the extracellular matrix of the liver but display differences in substrate specificity. These data not only identify Bacteroides found in bovine liver abscesses but also provide new insights into the potential role that these organisms may play in this production-limiting disease.

IMPORTANCE

Liver abscesses (LAs) are commonly found in cattle raised in feedlots and result from a bacterial infection of the liver. Not only are LAs a concern for animal health, but they also impact growth efficiency, animal welfare, and cost the North American beef industry upwards of $120 million per annum. Recently, it has been found that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides; however, to date, the biological relevance in LA pathogenesis and the identity of these bacteria are unknown. This research describes the isolation, identification, and genomic characterization of the Bacteroides found in bovine liver abscesses. These data provide a critical foundation for expanding our knowledge of the potential role Bacteroides play in liver abscess development and could contribute to the identification of novel targets for developing treatments to prevent this important production-limiting disease.

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.

Survey of gut microbial biogeography and their functional niche in the grow-finishing swine of ordinary feeding

Background

Swine represent one of the most economically significant livestock worldwide, and their intestinal microbial communities are crucial for maintaining physiological development and regulating host metabolism. While extensive research has focused on the fecal microbiota of swine, investigations into microbial communities across different intestinal segments remain limited.

Objective

This study aims to elucidate the intestinal microbiota of swine by analyzing luminal contents from different intestinal segments, including the duodenum, jejunum, ileum, cecum, and colon.

Methods

We employed 16S rRNA sequencing to explore the diversity and structure of gut microbial biogeography, microbial functional niches, and their associated pathways.

Results

Our findings reveal significantly lower microbial richness and diversity in the small intestine (duodenum, jejunum, and ileum) compared to the large intestine (cecum and colon) (p < 0.05). At the phylum level, Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the dominant phyla, collectively accounting for over 90% of the total sequences. In the small intestine, Proteobacteria (4.76-34.2%), Actinobacteria, and Fusobacteriota were more abundant, whereas in the large intestine, Firmicutes (89.8-90.4%) was predominated. At the genus level, Fusobacterium, Corynebacterium, Rothia, Bradyrhizobium, and Brevundimonas were predominant in duodenum. Romboutsia, Clostridium_sensu_stricto_1, Terrisporobacter, and Jeotgalicoccus demonstrated greater abundances in the jejunum and ileum. Oscillospiraceae_UCG-005 in the cecum and Christensenellaceae_R-7_group in the colon were more abundant with 16.4 and 20.2% relative abundances, respectively. The specialists detected from the duodenum to the colon were all the predominant genera in each intestinal segment with relatively higher relative abundance. For instance, Romboutsia (3.06-36.1%), Clostridium_sensu_stricto_1 (5.31-18.6%), and Terrisporobacter (0.849-5.72%) were dominant genera and specialists in the small intestine, associated with enriched pathways of Amino acid metabolism and Lipid metabolism. Conversely, Oscillospiraceae_UCG-005 (16.4%, 4.06%) and Christensenellaceae_R-7_group (5.44%, 20.2%) are predominant genera and specialists within the large intestine, linked to pathways involved in Glycan biosynthesis and metabolism pathway, as well as the Biosynthesis of other secondary metabolites.

Conclusion

These highlight the importance of genus specialists compared to genus generalists. The findings provide essential data for assessing the role of the intestinal microbiome in maintaining and enhancing swine health and productivity, offering fundamental guidance for further exploration of host-microbe interaction mechanisms and regulatory pathways.

Effects of peroxidized lipids on intestinal morphology, antioxidant capacity and gut microbiome in piglets

This study investigated the effect of peroxidized lipids on piglets' growth performance, intestinal morphology, inflammatory reactions, oxidative stress in the liver, duodenum, jejunum, ileum, and colon, and ileal microbiota. Twenty piglets (Duroc × [Landrace × Yorkshire]; age = 21 d old, BW = 6.5 ± 1 kg) were randomly assigned to two groups with 10 replicates per group and one piglet per replicate. The control group was fed 6% fresh soybean oil and the peroxidized soybean oil (PSO) group fed 6% PSO. The experimental feeding period lasted 24 d. The study found no impact on ADFI, ADG and gain to feed ratio (P > 0.05). However, the PSO group increased the diarrhea index and the serum levels of lactate dehydrogenase triglycerides, cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol (P < 0.05), along with decreased concentrations of alanine aminotransferase and blood urea nitrogen (P < 0.05). For oxidative enzymes, PSO increased the concentration of F2-isoprostane in urine (P = 0.032), malondialdehyde (MDA) in the duodenum (P = 0.001) and jejunum (P = 0.004), decreased thiobarbituric acid reactive substances (TBARS) in the liver (P = 0.001) but increased TBARS in duodenum (P = 0.001), and carbonylated proteins in the duodenum (P = 0.003). For antioxidant enzymes, PSO decreased superoxide dismutase (SOD) in the liver (P = 0.001), colon (P = 0.002), and jejunum (P = 0.015), along with glutathione peroxidase (GSH-Px) in the liver (P = 0.008) and NAD(P)H:quinone oxidoreductase 1 (NQO1) in ileum (P = 0.001). For inflammatory reactions, PSO increased interleukin (IL)-1β concentrations in the duodenum and colon, and IL-10 in the jejunum, while decreasing IL-4 concentration in the duodenum (P < 0.05). For intestinal morphology and ileal microbiota, PSO increased ileal crypt depth, while decreasing the crypt-to-villus ratio (P < 0.05). Peroxidized soybean oil increased the relative abundance of Prevotella, Clostridium_sensu_stricto_1, Clostridium_sensu_stricto_6, Pasteurella and Klebsiella (P < 0.05). In conclusion, this study revealed that PSO worsened diarrhea, increasing the ileal crypt depth and the relative abundance of harmful microbiota, and induced oxidative stress and inflammation in the intestines and liver, primarily in the jejunum and ileum.

Bacterial profiles of the oral, vaginal, and rectal mucosa and colostrum of periparturient sows

The commensal microbiota influences the health, feeding efficiency, and reproductive performance of sows. The microbiota composition in the alimentary and genitourinary tracts and in colostrum/milk during pregnancy and lactation also impacts the microbiota and immune system, growth, and health of the piglets. Knowledge of the microbial compositions is important for evaluation of these effects and for discovering ways to improve the health and productivity of the sows. Oral, vaginal, and rectal mucosa and colostrum were sampled from 32 sows of variable parity in late pregnancy, and colostrum within 6 hours of delivery of the first piglet, on four commercial piglet-producing farms in Finland. Microbial compositions were analyzed by 16S rRNA gene amplicon sequencing. The most abundant genera of the oral microbiota were Rothia, Moraxella, and Streptococcus. The rectal microbiota was dominated by Clostridium sensu stricto 1. Streptococcus was the most abundant genus in the vagina and colostrum. Moderate differences in diversity and composition were observed between farms. The relative abundances of the genera Neisseria (MaAsLin 2 q = 0.002, ANCOMBC q = 0.005), Fusobacterium (MaAsLin 2 q = 0.008, ANCOMBC q = 0.04) and Bacteroides (MaAsLin 2 q < 0.005, ANCOMBC q = 0.06) were lower in oral samples and Romboutsia (MaAsLin 2 q = 0.07, ANCOMBC q = 0.05), Turicibacter (MaAsLin 2 q = 0.08, ANCOMBC q = 0.02) and Lachnospiraceae_UCG_007 (MaAsLin 2 q = 0.1, ANCOMBC q = 0.05) were higher in rectal samples of multiparous compared to primiparous sows. In vaginal samples there was a tendency of higher relative abundances of the genera Fusobacterium and Streptococcus in multiparous than primiparous sows. Among the differentially abundant taxa, F. necrophorum and F. nucleatum were identified in oral samples, F. gastrosuis and F. necrophorum in vaginal samples, and S. dysgalactiae in colostrum samples. This study provides a comprehensive overview of the mucosal and colostrum microbiota of periparturient sows during normal production conditions on Finnish commercial farms.

Combined analysis of 16S rRNA gene sequencing data reveals core vaginal bacteria across livestock species

Investigating the livestock vaginal microbiota is of increasing interest due to its relationship with animal reproductive performance. Recent publications have uncovered a high degree of variability of the livestock vaginal microbiota, making it difficult to focus functional research on individual microorganisms. To address this variability, we conducted a combined analysis of publicly available 16S rRNA gene amplicon sequencing datasets to reveal the core vaginal microbiota in cattle, sheep, and pigs. The goal of this combined analysis was to identify bacterial genera that were shared despite a diverse overall sample population. A total of 2,911 vaginal samples (715 cattle, 964 sheep, and 1,232 pigs) from 29 different datasets were used in this combined analysis. Beta diversity analysis revealed structural differences of the vaginal microbiota between different animal species. Compositionally, the most abundant phyla were Bacillota, Pseudomonadota, and Bacteroidota. At the genus level, an unclassified Pasteurellaceae genus, Ureaplasma, and Streptococcus were the most abundant. Across the vaginal microbiota of individual livestock species, compositional differences were observed. The cattle and sheep vaginal microbiota contained a higher abundance of Ureaplasma and Histophilus whereas the pig vaginal microbiota contained more Fusobacterium and Parvimonas than that of the other livestock samples. Among the cattle, 120 OTUs and 82 genera were present in 70% of the vaginal samples. At the same threshold, pig samples had 40 core OTUs and 63 core genera, while the sheep samples had 22 core OTUs and 50 core genera. There were 19 overlapping core vaginal genera across the three animal species. The core vaginal OTUs were largely species-specific, although there were eight overlapping OTUs. These included Streptococcus (OTU 21), Clostridium sensu stricto 1 (OTU 18), and Corynebacterium (OTU 6), which were also some of the most abundant members of the livestock core vaginal microbiota. A better understanding of the livestock vaginal microbiota is required for future studies aimed at elucidation of the functional significance of individual microbes with respect to livestock reproductive efficiency. The core vaginal genera identified in this analysis will help guide research on mechanisms/pathways through which individual organisms enhance or impede animal reproductive efficiency.

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.

Effect of Gardeniae Fructus Powder on Growth Performance, Antioxidant Capacity, Intestinal Barrier Function, and Colonic Microbiota of Weaned Piglets

The present study aimed to explore the effect of GF powder on the growth performance, diarrhea rate, antioxidant and immune capacity, and intestinal health of weaned piglets. A total of 144 weaned piglets (8.29 ± 0.11 kg) at 21 d old were randomly assigned to four groups, with each treatment consisting of six replicate pens, with six piglets per pen, and each pen containing three barrows and three gilts. The piglets were fed a basal diet supplement with 0%, 0.4%, 0.6%, and 0.8% GF powder (n = 36). Our results indicated that compared with the basal diet, the F/G and diarrhea rate were remarkably decreased in the 0.8% GF group (p < 0.05). Serum biochemical parameters showed that supplementation with GF significantly increased the content of HDL-C (0.6 and 0.8% levels), IL-6 (0.8% level), IL-10 (0.4, 0.6, and 0.8% levels), Ig G (0.4% level), and Ig A (0.8% level) compared with the basal diet (p < 0.05). The index of antioxidant capacity showed that compared with a basal diet, supplementation with GF significantly decreased serum MDA content (0.4% and 0.8% levels) and jejunal and ileal MDA content (0.4%, 0.6%, and 0.8% levels) (p < 0.05). Additionally, compared with the basal diet, supplementation with GF significantly increased serum and ileal T-AOC content (0.4%, 0.6%, and 0.8% levels), serum T-SOD content (0.4% and 0.8% levels), ileal T-SOD content (0.4%, 0.6%, and 0.8% levels), CAT content (0.4%, 0.6%, and 0.8% levels), and jejunal GSH-Px content (0.8% level) (p < 0.05). The results of gene expression indicate that compared with the basal diet, supplementation with GF significantly increased Nrf 2 (0.4% level), NQO (0.4% level), SOD 1 (0.4% and 0.8% levels), and GCLC (0.4% level) and GCLM (0.8% level) abundance in jejunal mucosa; supplementation with GF significantly increased Nrf 2 (0.4%, 0.6%, and 0.8% levels), HO-1 (0.4% level), NQO (0.8% level), SOD 1 (0.4% and 0.8% levels), and GCLC (0.4% level) and GCLM (0.8% level) abundance in ileal mucosa (p < 0.05). Ulteriorly, the present results indicate that supplementation with GF at the 0.8% level significantly increased the villus height in the jejunum and ileum as well as the villus/crypt ratio in the ileum compared with the basal diet (p < 0.05). Compared with the basal diet, 0.4% GF significantly increased Occludin gene expression in ileal mucosa (p < 0.05), 0.6% GF significantly increased ZO-1, Claudin-1, and Occludin gene expression in jejunal mucosa (p < 0.05), and 0.8% GF significantly increased ZO-1 and Occludin gene expression in jejunal mucosa along with Occludin expression in ileal mucosa (p < 0.05). Furthermore, colonic microbiota composition showed that Shannon, observed species, and Chao 1 indices were significantly increased in the 0.8% GF group compared with the basal diet (p < 0.05). At the phylum level, in comparison with the basal diet, the relative abundance of Firmicutes significantly decreased in the 0.4%, 0.6%, and 0.8% GF groups, and Bacteroidetes increased in the 0.8% GF group (p < 0.05). At the genus level, compared with the basal diet, 0.6% and 0.8% GF significantly increased Prevotella abundance, and 0.6% GF significantly decreased Coprococcus abundance (p < 0.05). At the species level, compared with the basal diet, 0.8% GF significantly increased Prevotella copri abundance, and 0.4%, 0.6%, and 0.8% GF significantly decreased Blautia obeum abundance (p < 0.05). In summary, a dietary supplement with 0.8% Gardeniae Fructus powder significantly decreased the F/G and diarrhea rate and improved antioxidant capacity and intestinal barrier function, which may be associated with the improvement of the relative abundance of Prevotella copri. These findings indicate that Gardeniae Fructus powder may be used as a feed additive in swine weaning.

Fungi in the Gut Microbiota: Interactions, Homeostasis, and Host Physiology

The mammalian gastrointestinal tract is a stage for dynamic inter-kingdom interactions among bacteria, fungi, viruses, and protozoa, which collectively shape the gut micro-ecology and influence host physiology. Despite being a modest fraction, the fungal community, also referred to as mycobiota, represents a critical component of the gut microbiota. Emerging evidence suggests that fungi act as early colonizers of the intestine, exerting a lasting influence on gut development. Meanwhile, the composition of the mycobiota is influenced by multiple factors, with diet, nutrition, drug use (e.g., antimicrobials), and physical condition standing as primary drivers. During its establishment, the mycobiota forms both antagonistic and synergistic relationships with bacterial communities within the host. For instance, intestinal fungi can inhibit bacterial colonization by producing alcohol, while certain bacterial pathogens exploit fungal iron carriers to enhance their growth. However, the regulatory mechanisms governing these complex interactions remain poorly understood. In this review, we first introduce the methodologies for studying the microbiota, then address the significance of the mycobiota in the mammalian intestine, especially during weaning when all 'primary drivers' change, and, finally, discuss interactions between fungi and bacteria under various influencing factors. Our review aims to shed light on the complex inter-kingdom dynamics between fungi and bacteria in gut homeostasis and provide insights into how they can be better understood and managed to improve host health and disease outcomes.

Microbiota composition of an autochthonous Krškopolje pig breed reared in two different organic production systems

It has been shown that different production systems (conventional vs. pasture-raised pigs) and co-rearing of pigs with other livestock influence the gut microbiota composition in pigs. In this study, two independent trials were conducted to investigate the 16S fecal microbiota of the autochthonous Krškopolje pig. In each trial, three study groups were analyzed: (i) pasture-raised pigs cohabiting with small ruminants (group L1, farm 1), (ii) indoor-raised pigs without contact with other farm animals (group L2, farm 2) and fed the same commercial organic feed as the other two groups, and (iii) pasture-raised pigs cohabiting with cattle (group L3, farm 2). The pigs were sampled four times during the grower-finisher period, corresponding to the different seasons. A total of 18 and 22 pigs were included in trials 1 and 2, respectively. Alpha diversity was comparable between the study groups and the pigs of different age categories. The two predominant bacterial phyla in all three groups were Bacteroidota and Firmicutes. Significant differences in microbiota composition were found between pigs of different age categories in both trials (nonparametric MANOVA, p < 0.008). The microbiota composition of pigs from group L1 was significantly different from that of pigs from groups L2 and L3, whereas groups L2 and L3 tended to be more similar in both trials. The present results indicate that the trial and the farm of origin have a significant influence on the pig gut microbiota, and that their influence is more pronounced than that of the housing system.

Temporal dynamics in the composition of metabolically active bacteria and fungi in the ileo-cecal lymph nodes of suckling and newly weaned piglets

The early microbial colonization of the porcine gut is an important priming factor for gut and immune development. Nevertheless, little is known about the composition of microbes that translocate into the ileo-cecal lymph nodes (ICLN) in the neonatal phase. This study aimed to characterize age- and nutrition-related changes in the metabolically active bacterial and fungal composition of the ICLN in suckling and newly weaned piglets. Ten litters received only sow milk, while ten litters had access to creep feed from day of life (DoL) 10. Weaning occurred on DoL28. The ICLN were collected from 10 piglets/feeding group on each sampling day (DoL7, 14, 21, 28, 31 and 35) for RNA isolation, transcription into complementary DNA for 16 S rRNA and ITS2 amplicon sequencing. Age and weaning influenced the microbiome in the ICLN more than the nutrition during the suckling phase. Species richness and alpha-diversity of the bacterial but not fungal communities were increased on DoL7 and postweaning. Potential modes of action may have been linked to gut permeability at these ages and selective sampling by immune cells. Potential selective transfer of microbes may explain the dominance of Lactobacillus and Limosilactobacillus in the ICLN. Piglets that only drank sow milk comprised more Bacteroides in their ICLN on DoL35 compared to the creep fed piglets. Especially the role of fungi in the ICLN, including their mechanisms for translocation survival, needs further attention, as we detected metabolically active mold fungi and plant pathogens (e.g., Fusarium, Alternaria and Blumeria) in the ICLN.

The impact of host genetics on porcine gut microbiota composition excluding maternal and postnatal environmental influences

The gut microbiota of the pig is being increasingly studied due to its implications for host homeostasis and the importance of the pig as a meat source and biomedical model of human diseases. However, most studies comparing the microbiome between different breeds do not consider the influence of maternal environment during the colonization of the microbiota. The aim of the present study was to compare the gut microbiota during postnatal growth between two pig genotypes (purebred Iberian vs. crossbreds Iberian x Large White pigs), gestated in a single maternal environment (pure Iberian mothers) inseminated with heterospermic semen. Postnatally, piglets were maintained in the same environmental conditions, and their microbiota was studied at 60 and 210 days old. Results showed that age had the greatest influence on alpha and beta diversity, and genotype also affected beta diversity at both ages. There were differences in the microbiome profile between genotypes at the ASV and genus levels when jointly analyzing the total number of samples, which may help to explain phenotypical differences. When each time-point was analyzed individually, there were more differences at 210 days-old than 60 days-old. Fecal short-chain fatty acids (SCFA) were also affected by age, but not by genotype. These results may be a basis for further research on host genotype interactions with the gut microbiota.

Microbiota modulation by the inclusion of Tenebrio molitor larvae as alternative to fermented soy protein concentrate in growing pigs diet

Tenebrio molitor meal represents a promising protein source for animal nutrition due to its low environmental impact and high nutritional value. To date, there is limited data in the literature regarding the effects of Tenebrio molitor meal on the modulation of gut microbiota in growing animals, with most results focusing on poultry rather than pigs. The aim of this study was to evaluate the effects of replacing fermented soy protein concentrate with Tenebrio molitor meal on gut microbiota and feed digestibility in growing pigs. A total of 14 growing pigs (80 ± 2 days old) were randomly allotted to two groups: the control group (CON) was fed a commercial diet containing 4% fermented soy protein concentrate (48% crude protein), and the treatment group (TM) was fed a basal diet containing 5% of T. molitor larvae meal formulated to be isonitrogenous and isoenergetic. The study lasted 28 days. Animals were weekly weighted and feed refuse was routinely measured. Fecal, blood samples, and rectal swabs were collected for analysis. No differences were observed in growth and diet digestibility for the protein and lipid components throughout the trial. No differences in the serum concentrations of albumin, globulin, urea, and interleukin-6 were registered in both groups, suggesting an unaltered health status. The TM group showed a significant difference in the beta diversity index considering the total duration of the trial (treatment effect evaluated with PERMANOVA, R2 0.0771, p value = 0.0099) showing an increased abundance of Elusimicrobium spp. and a decrease in Asteroplasma spp. in TM compared to the CON group (p < 0.05). Obtained findings indicate that 5% T. molitor meal can be included as a partial replacement for soy in growing pig formula without impairing pig growth and gut microbiota composition.

Longitudinal Microbiome-based Interpretable Machine Learning for Identification of Time-Varying Biomarkers in Early Prediction of Disease Outcomes

Information generated from longitudinally-sampled microbial data has the potential to illuminate important aspects of development and progression for many human conditions and diseases. Identifying microbial biomarkers and their time-varying effects can not only advance our understanding of pathogenetic mechanisms, but also facilitate early diagnosis and guide optimal timing of interventions. However, longitudinal predictive modeling of highly noisy and dynamic microbial data (e.g., metagenomics) poses analytical challenges. To overcome these challenges, we introduce a robust and interpretable machine-learning-based longitudinal microbiome analysis framework, LP-Micro, that encompasses: (i) longitudinal microbial feature screening via a polynomial group lasso, (ii) disease outcome prediction implemented via machine learning methods (e.g., XGBoost, deep neural networks), and (iii) interpretable association testing between time points, microbial features, and disease outcomes via permutation feature importance. We demonstrate in simulations that LP-Micro can not only identify incident disease-related microbiome taxa but also offers improved prediction accuracy compared to existing approaches. Applications of LP-Micro in two longitudinal microbiome studies with clinical outcomes of childhood dental disease and weight loss following bariatric surgery yield consistently high prediction accuracy. The identified critical early predictive time points are informative and aligned with clinical expectations.

The influence of host genotype and gut microbial interactions on feed efficiency traits in pigs

Feed efficiency and growth performance are economically important traits in pigs. Precious studies have been revealed that both genetics and gut microbes could influence host phenotypes, however, the mechanisms by which they affect pig growth and feed efficiency remain poorly understood. In this study, 361 crossbred Duroc × (Landrace × Yorkshire) commercial pigs were genotyped using GeneSeek Porcine SNP50K BeadChip, and the microbiotas from fecal samples were acquired using microbial 16S rRNA gene sequencing technology to investigate the impact of host genetics and gut microorganisms on growth and feed efficiency. The results showed that the heritability and enterobacterial force ranged from 0.27 to 0.46 and 0 to 0.03, respectively. Genome-wide association studies (GWAS) identified seven significant SNPs to be associated with growth and feed efficiency, and several genes, including AIF1L, ASS1, and QRFP were highlighted as candidates for the analyzed traits. Additionally, microbiome-genome-wide association studies GWAS revealed potential links between CCAR2, EGR3, GSTM3, and GPR61 genes and the abundance of microorganisms, such as Trueperella, Victivallis, and Erysipelatoclostridium. In addition, six microbial genera linked to growth and feed efficiency were identified as follows Lachnospiraceae_UCG-005, Prevotellaceae_UCG-003, Prevotellaceae_NK3B31_group, Prevotella_1, Prevotella_9, and Veillonella. Our findings provide novel insights into the factors influencing host phenotypic complexity and identify potential microbial targets for enhancing pig feed efficiency through selective breeding. This could aid in the development of strategies to manipulate the gut microbiota to optimize growth rates and feed efficiency in pig breeding.

Uncovering new Firmicutes species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation

Metagenome-assembled genomes (MAGs) have contributed to identifying non-culturable microorganisms and understanding their ecological functions. MAGs offer an advantage in investigating sporulation-associated genes, especially given the difficulty of isolating many species residing in the gut microbiota of multiple hosts. Bacterial sporulation is a key survival mechanism with implications for pathogenicity and biotechnology. Here, we investigate MAGs from vertebrate hosts, emphasizing taxonomic identification and identifying sporulation-associated genes in potential novel species within the Firmicutes phylum. We identified potential new species in the classes Clostridia (Borkfalkiaceae, Lachnospiraceae, Monoglobaceae, and Oscillospiraceae families) and Bacilli (Bacillaceae and Erysipelotrichaceae families) through phylogenetic and functional pathway analyses, highlighting their sporulation potential. Our study covers 146 MAGs, 124 of them without refined taxonomic assignments at the family level. We found that Clostridia and Bacilli have unique sporulation gene profiles in the refined family MAGs for cattle, swine, poultry, and human hosts. The presence of genes related to Spo0A regulon, engulfment, and spore cortex in MAGs underscores fundamental mechanisms in sporulation processes in currently uncharacterized species with sporulation potential from metagenomic dark matter. Furthermore, genomic analyses predict sporulation potential based on gene presence, genome size, and metabolic pathways involved in spore formation. We emphasize MAGs covering families not yet characterized through the phylogenetic analysis, and with extensive potential for spore-forming bacteria within Clostridia, Bacilli, UBA4882, and UBA994 classes. These findings contribute to exploring spore-forming bacteria, which provides evidence for novel species diversity in multiple hosts, their adaptive strategies, and potential applications in biotechnology and host health.IMPORTANCESpores are essential for bacterial survival in harsh environments, facilitating their persistence and adaptation. Exploring sporulation-associated genes in metagenome-assembled genomes (MAGs) from different hosts contributes to clinical and biotechnological domains. Our study investigated the extent of genes associated with bacterial sporulation in MAGs from poultry, swine, cattle, and humans, revealing these genes in uncultivated bacteria. We identified potential novel Firmicutes species with sporulation capabilities through phylogenetic and functional analyses. Notably, MAGs belonging to Clostridia, Bacilli, and unknown classes, namely UBA4882 and UBA994, remained uncharacterized at the family level, which raises the hypothesis that sporulation would also be present in these genomes. These findings contribute to our understanding of microbial adaptation and have implications for microbial ecology, underlining the importance of sporulation in Firmicutes across different hosts. Further studies into novel species and their sporulation capability can contribute to bacterial maintenance mechanisms in various organisms and their applications in biotechnology studies.

Microbial-transcriptome integrative analysis of heat stress effects on amino acid metabolism and lipid peroxidation in poultry jejunum

Despite the significant threat of heat stress to livestock animals, only a few studies have considered the potential relationship between broiler chickens and their microbiota. Therefore, this study examined microbial modifications, transcriptional changes and host-microbiome interactions using a predicted metabolome data-based approach to understand the impact of heat stress on poultry. After the analysis, the host functional enrichment analysis revealed that pathways related to lipid and protein metabolism were elevated under heat stress conditions. In contrast, pathways related to the cell cycle were suppressed under normal environmental temperatures. In line with the transcriptome analysis, the microbial analysis results indicate that taxonomic changes affect lipid degradation. Heat stress engendered statistically significant difference in the abundance of 11 microorganisms, including Bacteroides and Peptostreptococcacea. Together, integrative approach analysis suggests that microbiota-induced metabolites affect host fatty acid peroxidation metabolism, which is correlated with the gene families of Acyl-CoA dehydrogenase long chain (ACADL), Acyl-CoA Oxidase (ACOX) and Acetyl-CoA Acyltransferase (ACAA). This integrated approach provides novel insights into heat stress problems and identifies potential biomarkers associated with heat stress.

A comparison of wild boar and domestic pig microbiota does not reveal a loss of microbial species but an increase in alpha diversity and opportunistic genera in domestic pigs

The microbiome of wild animals is believed to be co-evolved with host species, which may play an important role in host physiology. It has been hypothesized that the rigorous hygienic practices in combination with antibiotics and diets with simplified formulas used in the modern swine industry may negatively affect the establishment and development of the gut microbiome. In this study, we evaluated the fecal microbiome of 90 domestic pigs sampled from nine farms in Canada and 39 wild pigs sampled from three different locations on two continents (North America and Europe) using 16S rRNA gene amplicon sequencing. Surprisingly, the gut microbiome in domestic pigs exhibited higher alpha-diversity indices than wild pigs (P < 0.0001). The wild pig microbiome showed a lower Firmicutes-to-Bacteroidetes ratio and a higher presence of bacterial phyla Elusimicrobiota, Verrucomicrobiota, Cyanobacteria, and Fibrobacterota when compared to their domestic counterparts. At the genus level, the wild pig microbiome had enriched genera that were known for fiber degradation and short-chain fatty acid production. Interestingly, the phylum Fusobacteriota was only observed in domestic pigs. We identified 31 ASVs that were commonly found in the pig gut microbiome, regardless of host sources, which could be recognized as members of the core gut microbiome. Interestingly, we found five ASVs missing in domestic pigs that were prevalent in wild ones, whereas domestic pigs harbored 59 ASVs that were completely absent in wild pigs. The present study sheds light on the impact of domestication on the pig gut microbiome, including the gain of new genera, which might provide the basis to identify novel targets to manipulate the pig gut microbiome for improved health.

IMPORTANCE

The microbiome of pigs plays a crucial role in shaping host physiology and health. This study sought to identify if domestication and current rearing practices have resulted in a loss of co-evolved bacterial species by comparing the microbiome of wild boar and conventionally raised pigs. It provides a comparison of domestic and wild pigs with the largest sample sizes and is the first to examine wild boars from multiple sites and continents. We were able to identify core microbiome members that were shared between wild and domestic populations, and on the contrary to expectation, few microbes were identified to be lost from wild boar. Nevertheless, the microbiome of wild boars had a lower abundance of important pathogenic genera and was distinct from domestic pigs. The differences in the microbial composition may identify an opportunity to shift the microbial community of domestic pigs towards that of wild boar with the intent to reduce pathogen load.

Gastrointestinal microbiota and metabolites responses to dietary cereal grains in an adult pig model

Corn (C), wheat (W), and paddy rice (PR) are important energy sources and are commonly used in feed production for swine. This study mainly focuses on the variation and regularities of microbiota and metabolites in the gastrointestinal tract (GIT) of pigs in response to C, W, and PR. A total of 18 pigs were allotted into three dietary groups with six replicated pigs and received diets containing C, W, or PR as the sole energy source, respectively. The results showed that digestive parts significantly affected the diversity of microbial communities. Cereal grain sources significantly influenced the β-diversity of microbial communities in the colon and rectum. Campylobacterota and Proteobacteria are mainly distributed in the duodenum, Lactobacillus in the jejunum, and Bacteroidota in the colon and rectum. The W diet increased the Bacteroidota, Spirochaetota, and Prevotellaceae_NK3B31_group abundances and showed the highest concentrations of all short-chain fatty acids (SCFAs) in the hindgut. Fibrobacterota, Bacteroidota, Spirochaetota, Prevotellaceae_NK3B31_group, Prevotella, and Treponema in the colon or rectum were positively correlated with acetate, propionate, butyrate, and total SCFAs. These findings suggested that aerobic bacteria and facultative anaerobes in the foregut will gradually be replaced by anaerobes in the hindgut. The W diet had the best fermentability and was beneficial to the colonization of microbial communities that mainly used carbohydrates. The hindgut flora of the PR diet group may be more balanced with fewer potential pathogenic bacteria. Many microbial communities have been identified to contribute positively to the SCFA production of the hindgut. Collectively, our study revealed the spatial variation regularities of GIT microbial communities in an adult pig model and provided new insights into GIT microbiota and responses of metabolites to cereal grain diets.

Comparing Gut Microbial Composition and Functional Adaptations between SPF and Non-SPF Pigs

The gut microbiota is a key factor significantly impacting host health by influencing metabolism and immune function. Its composition can be altered by genetic factors, as well as environmental factors such as the host's surroundings, diet, and antibiotic usage. This study aims to examine how the characteristics of the gut microbiota in pigs, used as source animals for xenotransplantation, vary depending on their rearing environment. We compared the diversity and composition of gut microbiota in fecal samples from pigs raised in specific pathogen-free (SPF) and conventional (non-SPF) facilities. The 16S RNA metagenome sequencing results revealed that pigs raised in non-SPF facilities exhibited greater gut microbiota diversity compared to those in SPF facilities. Genera such as Streptococcus and Ruminococcus were more abundant in SPF pigs compared to non-SPF pigs, while Blautia, Bacteroides, and Roseburia were only observed in SPF pigs. Conversely, Prevotella was exclusively present in non-SPF pigs. It was predicted that SPF pigs would show higher levels of processes related to carbohydrate and nucleotide metabolism, and environmental information processing. On the other hand, energy and lipid metabolism, as well as processes associated with genetic information, cell communication, and diseases, were predicted to be more active in the gut microbiota of non-SPF pigs. This study provides insights into how the presence or absence of microorganisms, including pathogens, in pig-rearing facilities affects the composition and function of the pigs' gut microbiota. Furthermore, this serves as a reference for tracing whether xenotransplantation source pigs were maintained in a pathogen-controlled environment.

Microbial and Metabolic Profiling of Obese and Lean Luchuan Pigs: Implications for Phenotypic Divergence

Luchuan (LC) pigs are a Chinese breed renowned for their distinctive black and white coloring, superior meat quality and rapid reproduction, but their growth rate is slow. Over the course of approximately two decades of controlled breeding, the LC pigs maintained at the Shanghai Academy of Agricultural Sciences (Shanghai, China) have diverged into two phenotypes: one characterized by obesity (FLC) and the other by leanness (LLC). Recent studies indicate a correlation between microorganisms and the differentiation of host phenotypes. In this study, we examined the fecal microbiota profiles and serum metabolites of FLC and LLC pigs. The body weight, chest circumference, and alanine aminotransferase and aspartate aminotransferase enzyme activities were increased in the FLC pigs compared to the LLC pigs. Conversely, the levels of the Fusobacterium and Streptococcus genera were lower in the FLC pigs, while the number of Firmicutes, Lactobacillus, Phascolartobacterium, and Rikenellaceae_RC9_gut_group members were higher. A total of 52 metabolites were altered between the two groups, with many playing crucial roles in prolactin signaling, oocyte meiosis, and aldosterone-regulated sodium reabsorption pathways. The correlation analyses demonstrated a significant association between the modified microbiota and metabolites and the phenotypic variations observed in the LC pigs. Specifically, Jeotgalicoccus was positively correlated with the body weight and chest circumference, but was negatively correlated with metabolites such as 2-mercaptobenzothiazole and N1-pyrazin-2-yl-4-chlorobenzamide, which were positively associated with Bacteroides. These results provide compelling evidence for a novel relationship between the gut microbiome and metabolome in the phenotypic differentiation of LC pigs.

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

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

Effect of different doses of camelina cake inclusion as a substitute of dietary soyabean meal on growth performance and gut health of weaned pigs

Camelina cake (CAM) is a co-product proposed as an alternative protein source; however, piglet data are still limited. This study aimed to evaluate the effect of different doses of CAM in substitution of soyabean meal on the growth, health and gut health of weaned pigs. At 14 d post-weaning (d0), sixty-four piglets were assigned either to a standard diet or to a diet with 4 %, 8 % or 12 % of CAM. Piglets were weighed weekly. At d7 and d28, faeces were collected for microbiota and polyamine and blood for reactive oxygen metabolites (ROM) and thyroxine analysis. At d28, pigs were slaughtered, organs were weighed, pH was recorded on gut, colon was analysed for volatile fatty acids (VFA) and jejunum was used for morphological and gene expression analysis. Data analysis was carried out using a mixed model including diet, pen and litter as factors; linear and quadratic contrasts were tested. CAM linearly reduced the average daily gain from d0-d7, d0-d14, d0-d21 and d0-d28 (P ≤ 0·01). From d0-d7 increasing CAM linearly decreased feed intake (P = 0·04) and increased linearly the feed to gain (P = 0·004). CAM increased linearly the liver weight (P < 0·0001) and affected the cadaverine (P < 0·001). The diet did not affect the ROM, thyroxine, intestinal pH, VFA and morphology. All doses of CAM increased the α diversity indices at d28 (P < 0·05). CAM at 4 % promoted the abundance of Butyricicoccaceae_UCG-008. Feeding with CAM enhanced resilience in the gut microbiome and can be evaluated as a potential alternative protein source with dose-dependent limitations on piglet growth performance.

Supplementing infant milk formula with a multi-strain synbiotic and osteopontin enhances colonic microbial colonization and modifies jejunal gene expression in lactating piglets

A total of ninety-six weaned piglets were assigned to four dietary treatments in a 2 × 2 design. The treatments included: a standard milk formula (CTR); CTR + probiotics (6.4 × 108 cfu L-1Bifidobacterium longum subsp. infantis CECT 7210 and 1.1 × 108 cfu L-1Lactobacillus rhamnosus NH001) + prebiotics (galacto-oligosaccharides 4.36 g L-1 and human-milk-oligosaccharide 0.54 g L-1) (SYN); CTR + osteopontin (0.43 g L-1) (OPN); and CTR + SYN + OPN (CON). Daily records including feed intake, body weight, and clinical signs, were maintained throughout the 15-day trial. At the end of the study samples from blood, digestive content, and gut tissues were collected to determine serum TNF-α, intestinal fermentative activity (SCFA and ammonia), colonic microbiota (16S rRNA Illumina-MiSeq), histomorphology, and jejunal gene expression (Open-Array). No statistical differences were found in weight gain; however, the animals supplemented with osteopontin exhibited higher feed intake. In terms of clinical signs, synbiotic supplementation led to a shorter duration of diarrhoea episodes. Regarding gut health, the sequenced faecal microbiota revealed better control of potentially dysbiotic bacteria with the CON diet at day 15. In the colon compartment, a significant increase in SCFA concentration, a decrease in ammonia concentration, and a significant decrease in intraepithelial lymphocyte counts were particularly observed in CON animals. The supplemented diets were also associated with modified jejunal gene expression. The synbiotic combination was characterized by the upregulation of genes related to intestinal maturation (ALPI, SI) and nutrient transport (SLC13A1, SLC15A1, SLC5A1, SLC7A8), and the downregulation of genes related to the response to pathogens (GBP1, IDO, TLR4) or the inflammatory response (IDO, IL-1β, TGF-β1). Osteopontin promoted the upregulation of a digestive function gene (GCG). Correlational analysis between the microbiota population and various intestinal environmental factors (SCFA concentration, histology, and gene expression) proposes mechanisms of communication between the gut microbiota and the host. In summary, these results suggest an improvement in the colonic colonization process and a better modulation of the immune response when milk formula is supplemented with the tested synbiotic combined with osteopontin, benefiting from a synergistic effect.

Integration of metataxonomic data sets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables

The management of food fermentation is still largely based on empirical knowledge, as the dynamics of microbial communities and the underlying metabolic networks that produce safe and nutritious products remain beyond our understanding. Although these closed ecosystems contain relatively few taxa, they have not yet been thoroughly characterized with respect to how their microbial communities interact and dynamically evolve. However, with the increased availability of metataxonomic data sets on different fermented vegetables, it is now possible to gain a comprehensive understanding of the microbial relationships that structure plant fermentation. In this study, we applied a network-based approach to the integration of public metataxonomic 16S data sets targeting different fermented vegetables throughout time. Specifically, we aimed to explore, compare, and combine public 16S data sets to identify shared associations between amplicon sequence variants (ASVs) obtained from independent studies. The workflow includes steps for searching and selecting public time-series data sets and constructing association networks of ASVs based on co-abundance metrics. Networks for individual data sets are then integrated into a core network, highlighting significant associations. Microbial communities are identified based on the comparison and clustering of ASV networks using the "stochastic block model" method. When we applied this method to 10 public data sets (including a total of 931 samples) targeting five varieties of vegetables with different sampling times, we found that it was able to shed light on the dynamics of vegetable fermentation by characterizing the processes of community succession among different bacterial assemblages.

IMPORTANCE

Within the growing body of research on the bacterial communities involved in the fermentation of vegetables, there is particular interest in discovering the species or consortia that drive different fermentation steps. This integrative analysis demonstrates that the reuse and integration of public microbiome data sets can provide new insights into a little-known biotope. Our most important finding is the recurrent but transient appearance, at the beginning of vegetable fermentation, of amplicon sequence variants (ASVs) belonging to Enterobacterales and their associations with ASVs belonging to Lactobacillales. These findings could be applied to the design of new fermented products.

Carrier state of enterotoxigenic Escherichia coli virulence markers in pigs: Effects on gut microbiota modulation and immune markers transcription

Enterotoxigenic Escherichia coli (ETEC) causes diarrhea in pigs at early age, leading to high mortality rates and significant economic losses in the swine industry. ETEC effect on gut microbiota and immune system is mostly studied in diarrheic model under controlled laboratory conditions, however its impact on asymptomatic carriers remains unknown. Thus, we investigated whether ETEC can modulate gut microbiota or regulate the transcription of immune markers in asymptomatic pigs in farm environment. Stool samples from newborn piglets, nursery and growing pigs, and sows were screened for ETEC markers, then submitted to 16S-rDNA sequencing to explore gut microbiota composition in carriers (ETEC+) and non-carriers (ETEC-) animals. We observed a reduced α-diversity in ETEC+ animals (p < 0.05), while bacterial compositions were mostly driven by ageing (p > 0.05). Prevotella marked ETEC-carrier group, while Rikenellaceae RC9 gut group was a marker for a healthy gut microbiota, suggesting that they might be biomarker candidates for surveillance and supplementation purposes. Furthermore, we observed transcription regulation of il6 and tff2 genes in ETEC+ in newborn and nursery stages, respectively. Our findings indicate that ETEC presence modulate gut microbiota and the immune response in asymptomatic pigs; nevertheless, further studies using a probabilistic design must be performed to assess the effect of ETEC presence on gut imbalance in pigs despite the age bias.

Diversity and host interaction of the gut microbiota in specific pathogen-free pigs

Pigs are widely used as animal models in various studies related to humans. The interaction between the gut microbiota and the host has significant effects on the host's health and disease status. However, although there have been many studies investigating the pig gut microbiota, the findings have been inconsistent due to variations in rearing conditions. Interactions between the gut microbiota and host have not been fully explored in pigs. Specific pathogen-free (SPF) pigs are ideal non-primate large animals to study the interactions between the gut microbiota and the host. In this study, we performed high-throughput sequencing analysis of the gut microbiota and the gut tissue transcriptome of six SPF pigs to provide a systematic understanding of the composition, function, and spatial distribution of gut microbiota in SPF pigs. We identified significant differences in microbial diversity and functionality among different gastrointestinal tract sites. Metagenomics data analysis revealed significant differences in alpha diversity and beta diversity of microbiota in different gastrointestinal sites of SPF pigs. Additionally, transcriptomic data indicated significant differences in gene expression as well as KEGG and GO functional enrichment between the small intestine and large intestine. Furthermore, by combining microbial metagenomics and host transcriptomics analyses, specific correlations were found between gut microbiota and host genes. These included a negative correlation between the TCN1 gene and Prevotella dentalis, possibly related to bacterial metabolic pathways involving vitamin B12, and a positive correlation between the BDH1 gene and Roseburia hominis, possibly because both are involved in fatty acid metabolism. These findings lay the groundwork for further exploration of the co-evolution between the microbiota and the host, specifically in relation to nutrition, metabolism, and immunity. In conclusion, we have elucidated the diversity of the gut microbiota in SPF pigs and conducted a detailed investigation into the interactions between the gut microbiota and host gene expression. These results contribute to our understanding of the intricate dynamics between the gut microbiota and the host, offering important references for advancements in life science research, bioproduct production, and sustainable development in animal husbandry.

Increased Dietary Trp, Thr, and Met Supplementation Improves Performance, Health, and Protein Metabolism of Weaned Piglets under Mixed Management and Poor Housing Conditions

A sanitary challenge was carried out to induce suboptimal herd health while investigating the effect of amino acids supplementation on piglet responses. Weaned piglets of high sanitary status (6.33 ± 0.91 kg of BW) were distributed in a 2 × 2 factorial arrangement into two similar facilities with contrasting sanitary conditions and two different diets. Our results suggest that increased Trp, Thr, and Met dietary supplementation could support the immune systems of piglets under a sanitary challenge. In this manner, AA+ supplementation improved the performance and metabolism of piglets under mixed management and poor sanitary conditions. No major temporal microbiome changes were associated with differences in performance regardless of sanitary conditions or diets. Since piglets often become mixed in multiple-site production systems and facility hygiene is also often neglected, this study suggests that increased Trp, Thr, and Met (AA+) dietary supplementation could contribute to mitigating the side effects of these harmful risk factors in modern pig farms.

Effect of a probiotic and an antibiotic on the mobilome of the porcine microbiota

Introduction: To consider the growing health issues caused by antibiotic resistance from a "one health" perspective, the contribution of meat production needs to be addressed. While antibiotic resistance is naturally present in microbial communities, the treatment of farm animals with antibiotics causes an increase in antibiotic resistance genes (ARG) in the gut microbiome. Pigs are among the most prevalent animals in agriculture; therefore, reducing the prevalence of antibiotic-resistant bacteria in the pig gut microbiome could reduce the spread of antibiotic resistance. Probiotics are often studied as a way to modulate the microbiome and are, therefore, an interesting way to potentially decrease antibiotic resistance. Methods: To assess the efficacy of a probiotic to reduce the prevalence of ARGs in the pig microbiome, six pigs received either treatment with antibiotics (tylvalosin), probiotics (Pediococcus acidilactici MA18/5M; Biopower® PA), or a combination of both. Their faeces and ileal digesta were collected and DNA was extracted for whole genome shotgun sequencing. The reads were compared with taxonomy and ARG databases to identify the taxa and resistance genes in the samples. Results: The results showed that the ARG profiles in the faeces of the antibiotic and combination treatments were similar, and both were different from the profiles of the probiotic treatment (p < 0.05). The effects of the treatments were different in the digesta and faeces. Many macrolide resistance genes were detected in a higher proportion in the microbiome of the pigs treated with antibiotics or the combination of probiotics and antibiotics. Resistance-carrying conjugative plasmids and horizontal transfer genes were also amplified in faeces samples for the antibiotic and combined treatments. There was no effect of treatment on the short chain fatty acid content in the digesta or the faeces. Conclusion: There is no positive effect of adding probiotics to an antibiotic treatment when these treatments are administered simultaneously.

Effects of supplemental bacteriophage on the gut microbiota and nutrient digestibility of ileal-cannulated pigs

This study measured the potential changes of the microbiota in the gastrointestinal tract and energy and nutrient digestibility by supplemental bacteriophages in pigs. Twelve castrated male pigs (initial mean body weight = 29.5 ± 2.3 kg) were surgically cannulated using T-cannula. The animals were housed individually in pens equipped with a feeder and a nipple waterer. The pigs were allotted to 1 of 3 experimental diets in a quadruplicated 3 × 2 Latin square design with 3 experimental diets, 2 periods, and 12 pigs resulting in 8 replicates per diet. The 3 diets were a control mainly based on corn and soybean meal with no antibiotics or bacteriophages, a diet containing 0.1% antibiotics, and a diet containing 0.2% bacteriophages. On day 5 of the experimental period, feces were collected and on days 6 and 7, ileal digesta were collected. Genomic DNA for bacteria were extracted from the ileal digesta and feces and the V4 region of the 16S rRNA gene was amplified. The ileal and fecal digestibility of energy, dry matter, organic matter, crude protein, and fiber was unaffected by dietary antibiotics or bacteriophages. At the phylum level, the supplemental antibiotic or bacteriophage tended to result in a higher proportion of Firmicutes (p = 0.059) and a lower proportion of Bacteroidetes (p = 0.099) in the ileal digesta samples compared with the control group with no difference between the antibiotic and bacteriophage groups. At the genus level, the supplemental antibiotic or bacteriophage tended to result in a higher proportion of Lactobacillus (p = 0.062) and a lower proportion of Bacteroides (p = 0.074) and Streptococcus (p = 0.088) in the ileal digesta compared with the control group with no difference between the antibiotic and bacteriophage groups. In the feces, supplemental antibiotics or bacteriophages reduced the proportion of Bifidobacterium compared with the control group (p = 0.029) with no difference between the antibiotic and bacteriophage groups. Overall, supplemental antibiotics and bacteriophages showed positive effect on the microbiota of in the ileal digesta without largely affecting energy or nutrient digestibility, with no differences between the antibiotic and bacteriophage groups in growing pigs.

A comparative study of the bacterial diversity and composition of nursery piglets' oral fluid, feces, and housing environment

The oral cavity is the portal of entry for many microorganisms that affect swine, and the swine oral fluid has been used as a specimen for the diagnosis of several infectious diseases. The oral microbiota has been shown to play important roles in humans, such as protection against non-indigenous bacteria. In swine, studies that have investigated the microbial composition of the oral cavity of pigs are scarce. This study aimed to characterize the oral fluid microbiota of weaned pigs from five commercial farms in Brazil and compare it to their respective fecal and environmental microbiotas. Bacterial compositions were determined by 16S rRNA gene sequencing and analyzed in R Studio. Oral fluid samples were significantly less diverse (alpha diversity) than pen floor and fecal samples (P < 0.01). Alpha diversity changed among farms in oral fluid and pen floor samples, but no differences were observed in fecal samples. Permutational ANOVA revealed that beta diversity was significantly different among sample types (P = 0.001) and farms (P = 0.001), with separation of sample types (feces, pen floor, and oral fluid) on the principal coordinates analysis. Most counts obtained from oral fluid samples were classified as Firmicutes (80.4%) and Proteobacteria (7.7%). The genera Streptococcus, members of the Pasteurellaceae family, and Veillonella were differentially abundant in oral fluid samples when compared to fecal samples, in which Streptococcus was identified as a core genus that was strongly correlated (SparCC) with other taxa. Firmicutes and Bacteroidota were the most relatively abundant phyla identified in fecal and pen floor samples, and Prevotella_9 was the most classified genus. No differentially abundant taxa were identified when comparing fecal samples and pen floor samples. We concluded that under the conditions of our study, the oral fluid microbiota of weaned piglets is different (beta diversity) and less diverse (alpha diversity) than the fecal and environmental microbiotas. Several differentially abundant taxa were identified in the oral fluid samples, and some have been described as important colonizers of the oral cavity in human microbiome studies. Further understanding of the relationship between the oral fluid microbiota and swine is necessary and would create opportunities for the development of innovative solutions that target the microbiota to improve swine health and production.

Impact of precursor-derived peracetic acid on post-weaning diarrhea, intestinal microbiota, and predicted microbial functional genes in weaned pigs

Post-weaning diarrhea affects piglets in the nursery phase of production, leading to a substantial impact both at the farm and financial levels. The multifactorial etiology of this disease includes housing conditions, pig genetics, microbial composition, and metagenomic assets. Among the common therapeutic approaches, the widely used zinc oxide underwent a European Union ban in 2022 due to its negative environmental impact and correlation to increased antimicrobial resistance. During this study, we have tested two levels of inclusion of the potential antimicrobial alternative peracetic acid, delivered in water via the hydrolysis of the precursors sodium percarbonate and tetraacetylethylenediamine, in comparison to zinc oxide and an untreated control during a 2-week animal study. We assessed the microbial composition and predicted the metagenome, together with performance and physiological parameters, in order to describe the microbial functional role in etiopathology. Both zinc oxide and peracetic acid resulted in amelioration of the diarrheal status by the end of the trial period, with noticeable zinc oxide effects visible from the first week. This was accompanied by improved performance when compared to the first-week figures and a decreased stomach pH in both peracetic acid levels. A significant reduction in both stomach and caecal Proteobacteria was recorded in the zinc oxide group, and a significant reduction of Campylobacter in the stomach was reported for both zinc oxide and one of the peracetic acid concentrations. Among other functional differences, we found that the predicted ortholog for the zonula occludens toxin, a virulence factor present in pathogens like Escherichia coli and Campylobacter jejuni, was less abundant in the stomach of treated pigs compared to the control group. In water, peracetic acid delivered via precursor hydrolysis has the potential to be a valid intervention, an alternative to antimicrobial, to assist the weaning of piglets. Our findings support the view that post-weaning diarrhea is a complex multifactorial disease with an important metagenomic component characterized by the differential abundance of specific predicted orthologs and microbial genera in the stomach and caecum of pigs.

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

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

Estimating the contribution of the porcine fecal core microbiota to metabolite production via mathematical modeling and in vitro fermentation

The swine gut microbiota is a complex ecosystem found throughout the gastrointestinal tract, with multiple exchanges with the host and whose composition is linked to both external and internal factors, such as diet or breed. Diet, probiotic, or prebiotic interventions have been designed to boost beneficial host-microbiota interactions, such as the production of anti-inflammatory molecules, or the fermentation of otherwise undigested resources. In parallel, a smaller microbial population, shared among the same host species, independent of external or internal factors, has been described and defined as the "core microbiota." Therapies targeting the core microbiota could possibly lead to more precise and long-lasting effects. However, the metabolic role of the porcine core microbiota, especially in relation to the rest of the microbial community, is currently missing. We present here the first dynamic model of the porcine core microbiota, which we used to estimate the core-microbiota metabolite production and to forecast the effect of a synbiotic intervention targeting the core genera of the core microbiota. We developed a community model in which a total of 17 microbial groups were established based on culture-based information of representative species. First, the model parameters were estimated, and the resulting model simulations were compared favorably with in vitro experimentation. The model was then used to predict the microbial dynamics of the core and non-core members under different experimental conditions. Therefore, it was able to theorize the main-metabolite core microbiota contribution, hypothesizing that it could be mainly responsible for acetate and propionate, but not for butyrate production.IMPORTANCECurrently, little information is present in the literature to describe the generic metabolic role of the porcine core microbiota or to inform on the effect of interventions targeting the core genera. Moreover, both in vitro and in vivo experimentations aiming to explore the core microbiota dynamics are technically demanding, expensive, or restricted by ethical considerations. Modeling approaches can be used as an initial exploratory tool to develop hypotheses for targeted experimentation. Our mathematical model provides initial information on the microbial and metabolite dynamics of the core microbiota in relation to diet and therapeutic intervention.

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.

Effects of early postnatal gastric and colonic microbiota transplantation on piglet gut health

BACKGROUND

Diarrhea is a major cause of reduced growth and mortality in piglets during the suckling and weaning periods and poses a major threat to the global pig industry. Diarrhea and gut dysbiosis may in part be prevented via improved early postnatal microbial colonization of the gut. To secure better postnatal gut colonization, we hypothesized that transplantation of colonic or gastric content from healthy donors to newborn recipients would prevent diarrhea in the recipients in the post-weaning period. Our objective was to examine the impact of transplanting colonic or gastric content on health and growth parameters and paraclinical parameters in recipient single-housed piglets exposed to a weaning transition and challenged with enterotoxigenic Escherichia coli (ETEC).

METHODS

Seventy-two 1-day-old piglets were randomized to four groups: colonic microbiota transplantation (CMT, n = 18), colonic content filtrate transplantation (CcFT, n = 18), gastric microbiota transplantation (GMT, n = 18), or saline (CON, n = 18). Inoculations were given on d 2 and 3 of life, and all piglets were milk-fed until weaning (d 20) and shortly after challenged with ETEC (d 24). We assessed growth, diarrhea prevalence, ETEC concentration, organ weight, blood parameters, small intestinal morphology and histology, gut mucosal function, and microbiota composition and diversity.

RESULTS

Episodes of diarrhea were seen in all groups during both the milk- and the solid-feeding phase, possibly due to stress associated with single housing. However, CcFT showed lower diarrhea prevalence on d 27, 28, and 29 compared to CON (all P < 0.05). CcFT also showed a lower ETEC prevalence on d 27 (P < 0.05). CMT showed a higher alpha diversity and a difference in beta diversity compared to CON (P < 0.05). Growth and other paraclinical endpoints were similar across groups.

CONCLUSION

In conclusion, only CcFT reduced ETEC-related post-weaning diarrhea. However, the protective effect was marginal, suggesting that higher doses, more effective modalities of administration, longer treatment periods, and better donor quality should be explored by future research to optimize the protective effects of transplantation.

Meta-analysis reveals the predictable dynamic development of the gut microbiota in commercial pigs

IMPORTANCE

The swine gut microbiome undergoes an age-dependent assembly pattern with a developmental phase at early ages and a stabilization phase at later ages. Shorter time intervals and a wider range of data sources provided a clearer understanding of the gut microbiota colonization and succession and their associations with pig growth and development. The rapidly changing microbiota of suckling and weaning pigs implies potential time targets for growth and health regulation through gut microbiota manipulation. Since swine gut microbiota development is predictable, swine microbiota age can be calculated and compared between animal treatment groups rather than relying only on static time-matched comparisons.

Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates

Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.

Identification of intestinal and fecal microbial biomarkers using a porcine social stress model

Understanding the relationships between social stress and the gastrointestinal microbiota, and how they influence host health and performance is expected to have many scientific and commercial implementations in different species, including identification and improvement of challenges to animal welfare and health. In particular, the study of the stress impact on the gastrointestinal microbiota of pigs may be of interest as a model for human health. A porcine stress model based on repeated regrouping and reduced space allowance during the last 4 weeks of the finishing period was developed to identify stress-induced changes in the gut microbiome composition. The application of the porcine stress model resulted in a significant increase in salivary cortisol concentration over the course of the trial and decreased growth performance and appetite. The applied social stress resulted in 32 bacteria being either enriched (13) or depleted (19) in the intestine and feces. Fecal samples showed a greater number of microbial genera influenced by stress than caecum or colon samples. Our trial revealed that the opportunistic pathogens Treponema and Clostridium were enriched in colonic and fecal samples from stressed pigs. Additionally, genera such as Streptococcus, Parabacteroides, Desulfovibrio, Terrisporobacter, Marvinbryantia, and Romboutsia were found to be enriched in response to social stress. In contrast, the genera Prevotella, Faecalibacterium, Butyricicoccus, Dialister, Alloprevotella, Megasphaera, and Mitsuokella were depleted. These depleted bacteria are of great interest because they synthesize metabolites [e.g., short-chain fatty acids (SCFA), in particular, butyrate] showing beneficial health benefits due to inhibitory effects on pathogenic bacteria in different animal species. Of particular interest are Dialister and Faecalibacterium, as their depletion was identified in a human study to be associated with inferior quality of life and depression. We also revealed that some pigs were more susceptible to pathogens as indicated by large enrichments of opportunistic pathogens of Clostridium, Treponema, Streptococcus and Campylobacter. Generally, our results provide further evidence for the microbiota-gut-brain axis as indicated by an increase in cortisol concentration due to social stress regulated by the hypothalamic-pituitary-adrenal axis, and a change in microbiota composition, particularly of bacteria known to be associated with pathogenicity and mental health diseases.

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

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

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

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

Microbiota plasticity in tilapia gut revealed by meta-analysis evaluating the effect of probiotics, prebiotics, and biofloc

Tilapia species are among the most cultivated fish worldwide due to their biological advantages but face several challenges, including environmental impact and disease outbreaks. Feed additives, such as probiotics, prebiotics, and other microorganisms, have emerged as strategies to protect against pathogens and promote immune system activation and other host responses, with consequent reductions in antibiotic use. Because these additives also influence tilapia's gut microbiota and positively affect the tilapia culture, we assume it is a flexible annex organ capable of being subject to significant modifications without affecting the biological performance of the host. Therefore, we evaluated the effect of probiotics and other additives ingested by tilapia on its gut microbiota through a meta-analysis of several bioprojects studying the tilapia gut microbiota exposed to feed additives (probiotic, prebiotic, biofloc). A total of 221 tilapia gut microbiota samples from 14 bioprojects were evaluated. Alpha and beta diversity metrics showed no differentiation patterns in relation to the control group, either comparing additives as a group or individually. Results also revealed a control group with a wide dispersion pattern even when these fish did not receive additives. After concatenating the information, the tilapia gut core microbiota was represented by four enriched phyla including Proteobacteria (31%), Fusobacteria (23%), Actinobacteria (19%), and Firmicutes (16%), and seven minor phyla Planctomycetes (1%), Chlamydiae (1%), Chloroflexi (1%), Cyanobacteria (1%), Spirochaetes (1%), Deinococcus Thermus (1%), and Verrucomicrobia (1%). Finally, results suggest that the tilapia gut microbiota is a dynamic microbial community that can plastically respond to feed additives exposure with the potential to influence its taxonomic profile allowing a considerable optimal range of variation, probably guaranteeing its physiological function under different circumstances.

The difference of intestinal microbiota composition between Lantang and Landrace newborn piglets

BACKGROUND

The early development of intestinal microbiota plays a fundamental role in host health and development. To investigate the difference in the intestinal microbial composition between Lantang and Landrace newborn piglets, we amplified and sequenced the V3-V4 region of 16 S rRNA gene in jejunal microbiota of Lantang and landrace newborn.

RESULTS

The findings revealed that the dominant phyla in the jejunum of Lantang piglets were Firmicutes, Actinobacteria and Bacteroidetes, while the dominant phyla of Landrace is Proteobacteria and Fusobacteria. Specifically, Corynebacterium_1, Lactobacillus, Rothia, Granulicatella, Corynebacteriales_unclassified, Corynebacterium, Globicatella and Actinomycetales_unclassified were found to be the dominant genera of Lantang group, while Clostridium_sensu_stricto_1, Escherichia-Shigella, Actinobacillus and Bifidobacterium were the dominant genera of Landrace. Based on the functional prediction of bacteria, we found that bacterial communities from Lantang samples had a significantly greater abundance pathways of fatty acid synthesis, protein synthesis, DNA replication, recombination, repair and material transport across membranes, while the carrier protein of pathogenic bacteria was more abundant in Landrace samples.

CONCLUSIONS

Overall, there was a tremendous difference in the early intestinal flora composition between Landang and Landrace piglets, which was related to the breed characteristics and may be one of the reasons affecting the growth characteristics. However, more further extensive studies should be included to reveal the underlying relationship between early intestinal flora composition in different breeds and pig growth characteristics.

Salmonella enterica induces biogeography-specific changes in the gut microbiome of pigs

Swine are a major reservoir of an array of zoonotic Salmonella enterica subsp. enterica lineage I serovars including Derby, Typhimurium, and 4,[5],12:i:- (a.k.a. Monophasic Typhimurium). In this study, we assessed the gastrointestinal (GI) microbiome composition of pigs in different intestinal compartments and the feces following infection with specific zoonotic serovars of S. enterica (S. Derby, S. Monophasic, and S. Typhimurium). 16S rRNA based microbiome analysis was performed to assess for GI microbiome changes in terms of diversity (alpha and beta), community structure and volatility, and specific taxa alterations across GI biogeography (small and large intestine, feces) and days post-infection (DPI) 2, 4, and 28; these results were compared to disease phenotypes measured as histopathological changes. As previously reported, only S. Monophasic and S. Typhimurium induced morphological alterations that marked an inflammatory milieu restricted to the large intestine in this experimental model. S. Typhimurium alone induced significant changes at the alpha- (Simpson's and Shannon's indexes) and beta-diversity levels, specifically at the peak of inflammation in the large intestine and feces. Increased community dispersion and volatility in colonic apex and fecal microbiomes were also noted for S. Typhimurium. All three Salmonella serovars altered community structure as measured by co-occurrence networks; this was most prominent at DPI 2 and 4 in colonic apex samples. At the genus taxonomic level, a diverse array of putative short-chain fatty acid (SCFA) producing bacteria were altered and often decreased during the peak of inflammation at DPI 2 and 4 within colonic apex and fecal samples. Among all putative SCFA producing bacteria, Prevotella showed a broad pattern of negative correlation with disease scores at the peak of inflammation. In addition, Prevotella 9 was found to be significantly reduced in all Salmonella infected groups compared to the control at DPI 4 in the colonic apex. In conclusion, this work further elucidates that distinct swine-related zoonotic serovars of S. enterica can induce both shared (high resilience) and unique (altered resistance) alterations in gut microbiome biogeography, which helps inform future investigations of dietary modifications aimed at increasing colonization resistance against Salmonella through GI microbiome alterations.

Archaeome structure and function of the intestinal tract in healthy and H1N1 infected swine

Background

Methanogenic archaea represent a less investigated and likely underestimated part of the intestinal tract microbiome in swine.

Aims/Methods

This study aims to elucidate the archaeome structure and function in the porcine intestinal tract of healthy and H1N1 infected swine. We performed multi-omics analysis consisting of 16S rRNA gene profiling, metatranscriptomics and metaproteomics.

Results and discussion

We observed a significant increase from 0.48 to 4.50% of archaea in the intestinal tract microbiome along the ileum and colon, dominated by genera Methanobrevibacter and Methanosphaera. Furthermore, in feces of naïve and H1N1 infected swine, we observed significant but minor differences in the occurrence of archaeal phylotypes over the course of an infection experiment. Metatranscriptomic analysis of archaeal mRNAs revealed the major methanogenesis pathways of Methanobrevibacter and Methanosphaera to be hydrogenotrophic and methyl-reducing, respectively. Metaproteomics of archaeal peptides indicated some effects of the H1N1 infection on central metabolism of the gut archaea.

Conclusions/Take home message

Finally, this study provides the first multi-omics analysis and high-resolution insights into the structure and function of the porcine intestinal tract archaeome during a non-lethal Influenza A virus infection of the respiratory tract, demonstrating significant alterations in archaeal community composition and central metabolic functions.

Review: Effect of Experimental Diets on the Microbiome of Productive Animals

The microorganisms that inhabit the gastrointestinal tract are responsible for multiple chains of reactions that affect their environment and modify the internal metabolism, their study receives the name of microbiome, which has become more relevant in recent years. In the near future, the challenges related to feeding are anticipated to escalate, encompassing the nutritional needs to sustain an overpopulated world. Therefore, it is expected that a better understanding of the interactions between microorganisms within the digestive tract will allow their modulation in order to provide an improvement in the immune system, feed efficiency or the promotion of nutritional characteristics in production animals, among others. In the present study, the main effects of experimental diets in production animals were described, emphasizing the diversity of the bacterial populations found in response to the diets, ordering them between polygastric and monogastric animals, and then describing the experimental diets used and their effect on the microorganisms. It is hoped that this study will help as a first general approach to the study of the role of the microbiome in production animals under different diets.

Gastrointestinal Microbial Ecology of Weaned Piglets Fed Diets with Different Levels of Glyphosate

Glyphosate possesses antimicrobial properties, and the present study investigated potential effects of feed glyphosate on piglet gastrointestinal microbial ecology. Weaned piglets were allocated to four diets (glyphosate contents [mg/kg feed]: 0 mg/kg control [CON; i.e., basal diet with no glyphosate added], 20 mg/kg as Glyphomax commercial herbicide [GM20], and 20 mg/kg [IPA20] and 200 mg/kg [IPA200] as glyphosate isopropylamine [IPA] salt). Piglets were sacrificed after 9 and 35 days of treatment, and stomach, small intestine, cecum, and colon digesta were analyzed for glyphosate, aminomethylphosphonic acid (AMPA), organic acids, pH, dry matter content, and microbiota composition. Digesta glyphosate contents reflected dietary levels (on day 35, 0.17, 16.2, 20.5, and 207.5 mg/kg colon digesta, respectively). Overall, we observed no significant glyphosate-associated effects on digesta pH, dry matter content, and-with few exceptions-organic acid levels. On day 9, only minor gut microbiota changes were observed. On day 35, we observed a significant glyphosate-associated decrease in species richness (CON, 462; IPA200, 417) and in the relative abundance of certain Bacteroidetes genera: CF231 (CON, 3.71%; IPA20, 2.33%; IPA200, 2.07%) and g_0.24 (CON, 3.69%; IPA20, 2.07%; IPA200, 1.75%) in cecum. No significant changes were observed at the phylum level. In the colon, we observed a significant glyphosate-associated increase in the relative abundance of Firmicutes (CON, 57.7%; IPA20, 69.4%; IPA200, 66.1%) and a decrease in Bacteroidetes (CON, 32.6%; IPA20, 23.5%). Significant changes were only observed for few genera, e.g., g_0.24 (CON, 7.12%; IPA20, 4.59%; IPA200, 4.00%). In conclusion, exposing weaned piglets to glyphosate-amended feed did not affect gastrointestinal microbial ecology to a degree that was considered actual dysbiosis, e.g., no potential pathogen bloom was observed. IMPORTANCE Glyphosate residues can be found in feed made from genetically modified glyphosate-resistant crops treated with glyphosate or from conventional crops, desiccated with glyphosate before harvest. If these residues affect the gut microbiota to an extent that is unfavorable to livestock health and productivity, the widespread use of glyphosate on feed crops may need to be reconsidered. Few in vivo studies have been conducted to investigate potential impact of glyphosate on the gut microbial ecology and derived health issues of animals, in particular livestock, when exposed to dietary glyphosate residues. The aim of the present study was therefore to investigate potential effects on the gastrointestinal microbial ecology of newly weaned piglets fed glyphosate-amended diets. Piglets did not develop actual gut dysbiosis when fed diets, containing a commercial herbicide formulation or a glyphosate salt at the maximum residue level, defined by the European Union for common feed crops, or at a 10-fold-higher level.