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PDD Research Using Shotgun Analysis with ZnO and antibiotics in pigs

PDD Research Using Shotgun Analysis with ZnO and antibiotics in pigs

Postweaning diarrhea (PWD) is a relevant problem associated with early weaning on pig farms. In-feed antibiotics and therapeutic zinc oxide(ZnO), widely used to prevent PWD in piglets is now being banned by the EU. The Teagasc Pig Dept and colleagues published a recent paper on Shotgun Sequencing

Researchers: Juan M. Ortiz Sanjuán,a,b Edgar G. Manzanilla,a,c Raúl Cabrera-Rubio,d,e Fiona Crispie,d,e Paul D. Cotter,d,e,f Juan J. Garrido,b
Héctor Argüello, g

aPig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, County Cork, Ireland
bGrupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
cSchool of Veterinary Medicine, University College Dublin, Dublin, Ireland
dTeagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
eAPC Microbiome Institute, University College Cork, Cork, County Cork, Ireland
fVistaMilk SFI Research Centre, Fermoy, County Cork, Ireland
gAnimal Health Department, Veterinary Faculty, Universidad de León, León, Spain

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

Weaning and Postweaning diarrhea (PWD)

Weaning is a critical period, during which piglets are abruptly exposed to stressors such as an early separation from the mother, a sudden dietary change from milk to solid feed, and/or transport to a new environment where they are mixed with other litters.

Two major consequences of weaning are:

  • the piglets becoming immunocompromised and
  • a transient gut dysbiosis promoted by the sudden nutrient changes.

This is an opportunity for pathogens to colonize the gut and establish an infection, leading frequently to postweaning diarrhea (PWD), a multifactorial disease causing economic and productive losses on pig farms.

PWD usually involves the presence of enterotoxigenic Escherichia coli (ETEC) and requires antimicrobial therapies to control the problem.

Postweaning diarrhea (PWD) is a relevant problem associated with early weaning on pig farms. For decades, in-feed antibiotics and therapeutic zinc oxide (ZnO) have been widely used to prevent PWD in piglets.

The European Union is banning both strategies in 2022 due to antimicrobial resistance and environmental contamination concerns, respectively.

Understanding the effects of these products on the pig microbiome is crucial for correcting potential microbial disbalances that would prompt PWD.

By studying the modulation of the intestinal microbiota by ZnO and antibiotics, the potential exists to gain insights into the key changes that contribute to the control of PWD with a view to identifying other microbiome modulators than could be employed in the forthcoming post-ZnO and AB-free era.

Thus, the present study used shotgun sequencing to determine the impact of in-feed apramycin and therapeutic in-feed ZnO on the fecal microbiomes of early weaned pigs, while also assessing the relative importance of the background hygiene protocols in the facilities 

The trials

Using shotgun sequencing, three trials were carried out to explore the impact of in-feed apramycin and ZnO, combined with different farm hygiene protocols, on the fecal microbiomes of piglets 7 days postweaning.

In trial 1, 28-day-old piglets were allocated to one of three groups: control diet (Ct), Ct 1 ZnO (Zn), and Ct 1 apramycin (Ab).

In trials 2 and 3, piglets were allocated to the same treatments, but the trials also included different cleaning protocols, achieving different hygiene levels.

In-feed treatments impacted the richness, diversity, and relative abundance of the piglets’ microbiome more than hygiene.

Pigs in the Ct group showed higher species richness than pigs in the Ab and Zn groups.

A clustering analysis evidenced a link between Enterobacteriaceae in the Ct group; Lactobacillaceae and Veillonellaceae mainly in the Ct group; and Bacteroidaceae, Ruminococcaceae, Oscillospiraceae, Acidaminococcaceae, and Lactobacillaceae in the Ab and Zn groups.

Functional data analysis revealed a higher abundance of virulence genes in the Ct group microbiomes and heavy metal and antimicrobial resistance-related functions in the Zn treatment group.


The results demonstrate that alternatives to Ab and ZnO should balance the microbial abundance and stimulate the growth of beneficial gut inhabitants to outcompete potential pathogens. 

Read the full Research article here: Ortiz-SanJuan 2022 Shotgun analysis with ZnO and Antibiotics 

The Pig Development Department (PDD) issue an article on a topic of interest to pig producers on Fridays here on Teagasc Daily. Find out more here about the Teagasc Pig Development Department here