Using Shotgun Sequencing to Describe the Changes Induced by In-Feed Zinc Oxide and Apramycin in the Microbiomes of Pigs One Week Postweaning

Bacillus halotolerans attenuates inflammation induced by enterotoxigenic Escherichia coli infection in vivo and in vitro based on its metabolite soyasaponin I regulating the p105-Tpl2-ERK pathway

Soyasaponins, recognized for their anti-inflammatory and antioxidant effects, have not yet been fully explored for their role in combating enterotoxigenic Escherichia coli (ETEC) infections. Recent findings identified them in small-molecule metabolites of Bacillus, suggesting their broader biological relevance. This research screened 88 strains of B. halotolerans, identifying the strain BH M20221856 as significantly inhibitory against ETEC growth in vitro. It also reduced cellular damage and inflammatory response in IPEC-J2 cells. The antimicrobial activity of BH M20221856 was attributed to its small-molecule metabolites rather than secretory proteins. A total of 69 small molecules were identified from the metabolites of BH M20221856 using liquid chromatography mass spectrometry/mass spectrometry (LC-MS/MS). Among these, soyasaponin I (SoSa I) represented the largest multiple change in the enrichment analysis of differential metabolites and exhibited potent anti-ETEC effects in vivo. It significantly reduced the bacterial load of E. coli in mouse intestines, decreased serum endotoxin, D-lactic acid, and oxidative stress levels and alleviated intestinal pathological damage and inflammation. SoSa I enhanced immune regulation by mediating the p105-Tpl2-ERK signaling pathway. Further evaluations using transepithelial electrical resistance (TEER) and cell permeability assays showed that SoSa I alleviated ETEC-induced damage to epithelial barrier function. These results suggest that BH M20221856 and SoSa I may serve as preventative biologics against ETEC infections, providing new insights for developing strategies to prevent and control this disease.

Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs

BACKGROUND

Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD. New approaches to control PWD are needed, and understanding the role of the microbiota in this context is key. In this study, shotgun metagenome sequencing was used to describe the taxonomic and functional evolution of the faecal microbiota of the piglet during the first two weeks post weaning within three experimental groups, Ab, ZnO and no medication, on commercial farms using antimicrobials regularly in the post weaning period.

RESULTS

Diversity was affected by day post weaning (dpw), treatment used and diarrhoea but not by the farm. Microbiota composition evolved towards the dominance of groups of species such as Prevotella spp. at day 14dpw. ZnO inhibited E. coli overgrowth, promoted higher abundance of the family Bacteroidaceae and decreased Megasphaera spp. Animals treated with Ab exhibited inconsistent taxonomic changes across time points, with an overall increase of Limosilactobacillus reuteri and Megasphaera elsdenii. Samples from non-medicated pigs showed virulence-related functions at 7dpw, and specific ETEC-related virulence factors were detected in all samples presenting diarrhoea. Differential microbiota functions of pigs treated with ZnO were related to sulphur and DNA metabolism, as well as mechanisms of antimicrobial and heavy metal resistance, whereas Ab treated animals exhibited functions related to antimicrobial resistance and virulence.

CONCLUSION

Ab and particularly ZnO maintained a stable microbiota composition and functionality during the two weeks post weaning, by limiting E. coli overgrowth, and ultimately preventing microbiota dysbiosis. Future approaches to support piglet health should be able to reproduce this stable gut microbiota transition during the post weaning period, in order to maintain optimal gut physiological and productive conditions.

Salmonella Control in Swine: A Thoughtful Discussion of the Pre- and Post-Harvest Control Approaches in Industrialized Countries

Pork is among the major sources of human salmonellosis in developed countries. Since the 1990s, different surveys and cross-sectional studies, both national and international (i.e., the baseline studies performed in the European Union), have revealed and confirmed the widespread non-typhoidal Salmonella serotypes in pigs. A number of countries have implemented control programs with different approaches and degrees of success. The efforts could be implemented either at farms, in post-harvest stages, or both. The current review revises the current state of the art in Salmonella in swine, the control programs ongoing or conducted in the past, and their strengths and failures, with particular attention to the weight of pre- and post-harvest control and the implications that both have for the success of interventions or mitigation after outbreaks. This review provides a novel perspective on Salmonella control in swine, a matter that still includes uncertainties and room for improvement as a question of public health and One Health.

Interactions between maternal parity and feed additives drive the composition of pig gut microbiomes in the post-weaning period

BACKGROUND

Nursery pigs undergo stressors in the post-weaning period that result in production and welfare challenges. These challenges disproportionately impact the offspring of primiparous sows compared to those of multiparous counterparts. Little is known regarding potential interactions between parity and feed additives in the post-weaning period and their effects on nursery pig microbiomes. Therefore, the objective of this study was to investigate the effects of maternal parity on sow and offspring microbiomes and the influence of sow parity on pig fecal microbiome and performance in response to a prebiotic post-weaning. At weaning, piglets were allotted into three treatment groups: a standard nursery diet including pharmacological doses of Zn and Cu (Con), a group fed a commercial prebiotic only (Preb) based on an Aspergillus oryzae fermentation extract, and a group fed the same prebiotic plus Zn and Cu (Preb + ZnCu).

RESULTS

Although there were no differences in vaginal microbiome composition between primiparous and multiparous sows, fecal microbiome composition was different (R2 = 0.02, P = 0.03). The fecal microbiomes of primiparous offspring displayed significantly higher bacterial diversity compared to multiparous offspring at d 0 and d 21 postweaning (P < 0.01), with differences in community composition observed at d 21 (R2 = 0.03, P = 0.04). When analyzing the effects of maternal parity within each treatment, only the Preb diet triggered significant microbiome distinctions between primiparous and multiparous offspring (d 21: R2 = 0.13, P = 0.01; d 42: R2 = 0.19, P = 0.001). Compositional differences in pig fecal microbiomes between treatments were observed only at d 21 (R2 = 0.12, P = 0.001). Pigs in the Con group gained significantly more weight throughout the nursery period when compared to those in the Preb + ZnCu group.

CONCLUSIONS

Nursery pig gut microbiome composition was influenced by supplementation with an Aspergillus oryzae fermentation extract, with varying effects on performance when combined with pharmacological levels of Zn and Cu or for offspring of different maternal parity groups. These results indicate that the development of nursery pig gut microbiomes is shaped by maternal parity and potential interactions with the effects of dietary feed additives.

Fine-tuning of post-weaning pig microbiome structure and functionality by in-feed zinc oxide and antibiotics use

Introduction

Post-weaning diarrhoea (PWD) is a multifactorial disease that affects piglets after weaning, contributing to productive and economic losses. Its control includes the use of in-feed prophylactic antibiotics and therapeutic zinc oxide (ZnO), treatments that, since 2022, are no longer permitted in the European Union due to spread of antimicrobial resistance genes and pollution of soil with heavy metals. A dysbiosis in the microbiota has been suggested as a potential risk factor of PWD onset. Understanding pig's microbiota development around weaning and its changes in response to ZnO and antibiotics is crucial to develop feasible alternatives to prophylactic and metaphylactic antimicrobial use.

Methods

This study used shotgun metagenomic sequencing to investigate the environmental and faecal microbiota on 10 farms using (Treated) or not using (ZnO-free) in-feed antibiotics and ZnO during the first 14 days post-weaning (dpw). Environmental samples from clean pens were collected at weaning day (0dpw), and faecal samples at 0, 7 and 14dpw. Diarrhoeic faecal samples were collected at 7dpw when available.

Results

The analysis of data revealed that the faecal microbiota composition and its functionality was impacted by the sampling time point (microbiota maturation after weaning) but not by the farm environment. Treatment with antibiotics and ZnO showed no effects on diversity indices while the analyses of microbiota taxonomic and functional profiles revealed increased abundance of taxa and metabolic functions associated with Phascolarctobacterium succinatutens or different species of Prevotella spp. on the Treated farms, and with Megasphaera elsdenii and Escherichia coli on the ZnO-free farms. The analysis of diarrhoea samples revealed that the treatment favoured the microbiota transition or maturation from 0dpw to 14dpw in Treated farms, resembling the composition of healthy animals, when compared to diarrhoea from ZnO-free farms, which were linked in composition to 0dpw samples.

Discussion

The results provide a comprehensive overview of the beneficial effects of ZnO and antibiotics in PWD in the microbiota transition after weaning, preventing the overgrowth of pathogens such as pathogenic E. coli and revealing the key aspects in microbiota maturation that antibiotics or ZnO alternatives should fulfil.

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.

Blend of natural and natural identical essential oil compounds as a strategy to improve the gut health of weaning pigs

Weaning is one of the most critical phases in pig's life, often leading to postweaning diarrhoea (PWD). Zinc oxide (ZnO), at pharmacological doses, has been largely used to prevent PWD; however, due to antimicrobial co-resistant and environmental pollution issues, the EU banned its use in June 2022. Natural or natural identical components of essential oils and their mixture with organic acids are possible alternatives studied for their antimicrobial, anti-inflammatory and antioxidant abilities. This study aimed to evaluate the effect of two blends of natural or natural identical components of essential oils and organic acids compared to ZnO on health, performance, and gut health of weaned pigs. At weaning (d0), 96 piglets (7 058 ± 895 g) were assigned to one of four treatments balanced for BW and litter: CO (control treatment), ZnO (2 400 mg/kg ZnO from d0 to d14); Blend1 (cinnamaldehyde, ajowan and clove essential oils, 1 500 mg/kg feed); Blend2 (cinnamaldehyde, eugenol and short- and medium-chain fatty acids, 2 000 mg/kg feed). Pigs were weighed weekly until d35. Faeces were collected at d13 and d35 for microbiota (v3-v4 regions of the 16 s rRNA gene) and Escherichia coli (E. coli) count analysis. At d14 and d35, eight pigs/treatment were slaughtered; pH was recorded on intestinal contents and jejunal samples were collected for morphological and gene expression analysis. From d7-d14, the Blend2 had a lower average daily gain (ADG) than CO and ZnO (P < 0.05). ZnO and Blend1 never differed in ADG and feed intake. At d14, ZnO had a lower caecum pH than all other treatments. The CO treatment had a higher abundance of haemolytic E. coli than Blend1 (P = 0.01). At d13, the ZnO treatment had a lower alpha diversity (P < 0.01) and a different microbial beta diversity (P < 0.001) compared to the other treatments. At d13, the ZnO treatment was characterised by a higher abundance of Prevotellaceae_NK3B31_group (Linear Discriminant Analysis (LDA) score = 4.5, P = 0.011), Parabacteroides (LDA score = 4.5, P adj. = 0.005), the CO was characterised by Oscillospiraceae UCG-005 (LDA score = 4.3, P adj. = 0.005), Oscillospiraceae NK4A214_group (LDA score = 4.2, P adj. = 0.02), the Blend2 was characterised by Megasphaera (LDA score = 4.1, P adj. = 0.045), and Ruminococcus (LDA score = 3.9, P adj. = 0.015) and the Blend1 was characterised by Christensenellaceae_R-7_group (LDA score = 4.6, P adj. < 0.001) and Treponema (LDA score = 4.5, P adj. < 0.001). In conclusion, Blend1 allowed to maintain the gut health of postweaning piglets through modulation of the gut microbiome, the reduction of haemolytic E. coli while Blend2 did not help piglets.