Experimental facility had a greater effect on growth performance, gut microbiome, and metabolome in weaned pigs than feeding diets containing subtherapeutic levels of antibiotics: A case study

Michaela P. Trudeau, Wes Mosher, Huyen Tran, Brenda de Rodas, Theodore P. Karnezos, Pedro E. Urriola, Andres Gomez, Milena Saqui-Salces, Chi Chen, Gerald C. Shurson

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1 Scopus citations


The objective of this study was to define changes in the intestinal metabolome and microbiome associated with growth performance of weaned pigs fed subtherapeutic concentrations of antibiotics. Three experiments with the same antibiotic treatments were conducted on the same research farm but in two different facilities (nursery and wean-finish) using pigs weaned at 20-days of age from the same source herd and genotype, and fed the same diets formulated without antibiotics (NC) or with 0.01% chlortetracycline and 0.01% sulfamethazine (AB). Pigs were weighed and feed disappearance was determined on days (d) 10, 21, and 42 post-weaning to calculate average daily gain (ADG), average daily feed intake (ADFI), and gain:feed (G:F). On d 42, one pig/pen was selected for blood and ileal and cecal content collection. Targeted and untargeted metabolomic profiles were determined in serum and cecal contents using liquid chromatography-mass spectrometry, and composition of bacterial communities in intestinal content samples was determined by sequencing the V4 region of the 16s rRNA gene. Metabolomics and microbiome data were analyzed using diverse multivariate and machine learning methods. Pigs fed AB had significantly greater (P < 0.05) overall ADG and ADFI compared with those fed NC, and pig body weight, ADG, and G:F were also significantly different (P < 0.05) between experiments. Differences (P < 0.05) in serum metabolome along with ileal and cecal microbiome beta diversity were observed between experiments, but there were no differences in microbiome alpha diversity between experiments or treatments. Bacteria from the families Clostridiaceae, Streptomycetaceae, Peptostreptomycetaceae, and Leuconostocaceae were significant biomarkers for the AB treatment. In addition, pigs fed AB had increased serum arginine, histidine, lysine, and phenylalanine concentrations compared with NC. Percentage error from a random forest analysis indicated that most of the variation (8% error) in the microbiome was explained by the facility where the experiments were conducted. These results indicate that facility had a greater effect on growth performance, metabolome, and microbiome responses than feeding diets containing subtherapeutic levels of antibiotics.

Original languageEnglish (US)
Article numbere0285266
JournalPloS one
Issue number8 August
StatePublished - Aug 2023

Bibliographical note

Funding Information:
Partial research funding for conducting animal experiments was provided by Land O’ Lakes/Purina and managed by BdR. Additional funding provided by Land O’ Lakes/Purina to the University of Minnesota was managed by GCS for metabolomics and microbiome analysis and Research Assistantship support for MPT. BdR, TK, and HT from Land O’ Lakes/Purina were involved in study design, data collection and analysis, decision to publish, and preparation of the manuscript. The authors thank Margaret Schmidt, Jason Koch, and Kristy Segelhorst for assistance in maintaining and handling experimental animals, and data and tissue collection.

Publisher Copyright:
© 2023 Trudeau et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't


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