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

PeerJ

article

Rachel Gilroy¹  Anuradha Ravi¹  Maria Getino²  Isabella Pursley²  Daniel L. Horton²  Nabil-Fareed Alikhan¹  Dave Baker¹  Karim Gharbi³  Neil Hall³  Mick Watson⁵  Evelien M. Adriaenssens¹  Ebenezer Foster-Nyarko¹  Sheikh Jarju⁶  Arss Secka⁷  Martin Antonio⁶  Aharon Oren⁸  Roy R. Chaudhuri⁹  Roberto La Ragione²  Falk Hildebrand¹  Mark J. Pallen¹ 

[1] Quadram Institute Bioscience;School of Veterinary Medicine, University of Surrey;Earlham Institute, Norwich Research Park;University of East Anglia;Roslin Institute, University of Edinburgh;Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine;West Africa Livestock Innovation Centre;Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Hebrew University of Jerusalem;Department of Molecular Biology and Biotechnology, University of Sheffield

关键词: Chickens;    Gut microbiome;    Biodiversity;    Metagenomics;    Metagenome-assembled genome;    Bacterial nomenclature;    Uncultured bacteria;    Candidatus;   

DOI  :  10.7717/peerj.10941

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY