The fecal microbiota of piglets during weaning transition and its association with piglet growth across various farm environments

PLoS One. 2021 Apr 27;16(4):e0250655. doi: 10.1371/journal.pone.0250655. eCollection 2021.

Abstract

This study describes the fecal microbiota from piglets reared in different living environments during the weaning transition, and presents the characteristics of microbiota associated with good growth of piglets after weaning. Fecal samples were collected pre- (d26) and post-weaning (d35) from 288 male piglets in 16 conventional indoor commercial farms located in the West of France. The changes one week after weaning on the most abundant microbial families was roughly the same in all farms: alpha diversity increased, the relative abundance of Bacteroidaceae (-61%), Christensenellaceae (-35%), Enterobacteriaceae (-42%), and Clostridiaceae (-32%) decreased, while the relative abundance of Prevotellaceae (+143%) and Lachnospiraceae (+21%) increased. Among all the collected samples, four enterotypes that were ubiquitous in all farms were identified. They could be discriminated by their respective relative abundances of Prevotella, Faecalibacterium, Roseburia, and Lachnospira, and likely corresponded to a gradual maturational shift from pre- to post-weaning microbiota. The rearing environment influenced the frequency of enterotypes, as well as the relative abundance of 6 families at d26 (including Christensenellaceae and Lactobacillaceae), and of 21 families at d35. In all farms, piglets showing the highest relative growth rate during the first three weeks after weaning, which were characterized as more robust, had a higher relative abundance of Bacteroidetes, a lower relative abundance of Proteobacteria, and showed a greater increase in Prevotella, Coprococcus, and Lachnospira in the post-weaning period. This study revealed the presence of ubiquitous enterotypes among the farms of this study, reflecting maturational stages of microbiota from a young suckling to an older cereal-eating profile. Despite significant variation in the microbial profile between farms, piglets whose growth after weaning was less disrupted were, those who had reached the more mature phenotype characterized by Prevotella the fastest.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aging
  • Animal Feed / microbiology*
  • Animals
  • Bacteroidaceae / genetics
  • Bacteroidaceae / isolation & purification
  • Bacteroidetes / genetics
  • Bacteroidetes / isolation & purification
  • Farms
  • Feces / microbiology*
  • Gastrointestinal Microbiome*
  • Lactobacillaceae / genetics
  • Lactobacillaceae / isolation & purification
  • Male
  • RNA, Ribosomal, 16S / genetics
  • RNA, Ribosomal, 16S / metabolism
  • Swine
  • Weaning

Substances

  • RNA, Ribosomal, 16S

Grants and funding

This experiment was supported by: - the Integrated Management of Animal Health program of INRAE (GISA-SEVROBUST project) https://www6.inrae.fr - a grant from the Region Pays de la Loire (Sant’Innov project) https://www.psdrgo.org/PSDR4-en-Grand-Ouest/Les-projets/SANT-INNOV - a COST Action FA1401 (European Cooperation in Science and Technology) for the training of AB and DL. https://www.cost.eu/actions/FA1401 - Cooperl Arc Atlantique provided support in the form of salaries for one of the authors [AB], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of this author are articulated in the ‘author contributions’ section. https://www.cooperl.com None of the funders played a role in the study design and data analysis.