Assembly of hundreds of novel bacterial genomes from the chicken caecum

Laura Glendinning, Robert Stewart, Mark J. Pallen, Kellie Watson, Mick Watson

Research output: Contribution to journalArticlepeer-review


Background: Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short chain fatty acids, nitrogen recycling and amino acid production. In this study we sequence DNA from caecal contents samples taken from 24 chickens belonging to either a fast or slower growing breed consuming either a vegetable-only diet or a diet containing fish meal.
Results: We utilize 1.6T of Illumina data to construct 469 draft metagenome assembled bacterial genomes, including 460 novel strains, 283 novel species and 42 novel genera. We compare our genomes to data from nine European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome.
This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota
Original languageEnglish
Article number34 (2020)
Pages (from-to)1-16
JournalGenome Biology
Issue number34
Early online date12 Feb 2020
Publication statusE-pub ahead of print - 12 Feb 2020


  • Microbiota
  • Chicken
  • Metagenome
  • Microbial ecology
  • MAG
  • Caeca


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