Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

Rachel Gilroy, Anuradha Ravi, Maria Getino, Isabella Pursley, Daniel L. Horton, Nabil Fareed Alikhan, Dave Baker, Karim Gharbi, Neil Hall, Mick Watson, Evelien M. Adriaenssens, Ebenezer Foster-Nyarko, Sheikh Jarju, Arss Secka, Martin Antonio, Aharon Oren, Roy R. Chaudhuri, Roberto La Ragione, Falk Hildebrand*, Mark J. Pallen*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

70 Scopus citations


Background: The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. Results: We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii. Conclusions: Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.

Original languageAmerican English
Article numbere10941
StatePublished - 6 Apr 2021

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  • Bacterial nomenclature
  • Biodiversity
  • Candidatus
  • Chickens
  • Gut microbiome
  • Metagenome-assembled genome
  • Metagenomics
  • Uncultured bacteria


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