Gut Microbial Dynamics during Conventionalization of Germfree Chicken

mSphere. 2019 Mar 27;4(2):e00035-19. doi: 10.1128/mSphere.00035-19.


A gnotobiotic Gallus gallus (chicken) model was developed to study the dynamics of intestinal microflora from hatching to 18 days of age employing metagenomics. Intestinal samples were collected from a local population of feral chickens and administered orally to germfree 3-day-old chicks. Animals were euthanized on days 9 and 18 postinoculation, and intestinal samples were collected and subjected to metagenomic analysis. On day 18, the five most prevalent phyla were Bacteroidetes (43.03 ± 3.19%), Firmicutes (38.51 ± 2.67%), Actinobacteria (6.77 ± 0.7%), Proteobacteria (6.38 ± 0.7%), and Spirochaetes (2.71 ± 0.55%). Principal-coordinate analysis showed that the day 18 variables clustered more closely than the day 9 variables, suggesting that the microbial communities had changed temporally. The Morista-Horn index values ranged from 0.7 to 1, indicating that the communities in the inoculum and in the day 9 and day 18 samples were more similar than dissimilar. The predicted functional profiles of the microbiomes of the inoculum and the day 9 and day 18 samples were also similar (values of 0.98 to 1). These results indicate that the gnotobiotic chicks stably maintained the phylogenetic diversity and predicted metabolic functionality of the inoculum community.IMPORTANCE The domestic chicken is the cornerstone of animal agriculture worldwide, with a flock population exceeding 40 billion birds/year. It serves as an economically valuable source of protein globally. The microbiome of poultry has important effects on chicken growth, feed conversion, immune status, and pathogen resistance. The aim of our research was to develop a gnotobiotic chicken model appropriate for the study chicken gut microbiota function. Our experimental model shows that young germfree chicks are able to colonize diverse sets of gut bacteria. Therefore, besides the use of this model to study mechanisms of gut microbiota interactions in the chicken gut, it could be also used for applied aspects such as determining the safety and efficacy of new probiotic strains derived from chicken gut microbiota.

Keywords: Salmonella; competetive exclusion; feral chicken; gnotobiotic; metagenome; microbiota.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Bacteria / classification*
  • Bacteria / isolation & purification
  • Bacteroidetes / classification
  • Bacteroidetes / isolation & purification
  • Chickens / growth & development
  • DNA, Bacterial / genetics
  • Firmicutes / classification
  • Firmicutes / isolation & purification
  • Gastrointestinal Microbiome*
  • Gastrointestinal Tract / microbiology
  • Germ-Free Life*
  • Host Microbial Interactions*
  • Metagenomics
  • Phylogeny
  • Principal Component Analysis
  • RNA, Ribosomal, 16S / genetics


  • DNA, Bacterial
  • RNA, Ribosomal, 16S