A Genomic Census of the Chicken Gut Microbiome using Metagenomics and Culture

Abstract

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 deliver a genomic blueprint of 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 the chicken gut associated microbiome to date, encompassing dozens of novel candidate bacterial genera and hundreds of novel candidate species. Keen 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 faeces, documenting thirty 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 provides a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.

Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples

“…While 16S studies are more affordable, these studies in general do not have specificity at the bacterial species levels. Additionally, they are still capable of detecting changes in the abundance and diversity of bacterial genera [ 21 , 22 , 68 , 69 , 70 ]. Total DNA-based metagenomics provides higher resolution than 16S ribosomal amplicon sequencing for bacteria identification but involves larger, more complex, and expensive protocols.…”

“…ntNGS is now advancing as a powerful tool for farm-animal diagnostics [21][22][23][24][25] because it can identify and simultaneously genetically characterize multiple agents for each sample. Technical and logistic challenges are rapidly being resolved and one can envision that it will not be long before every farm will periodically obtain a report providing the "microbiological status" of the farm based on random or non-targeted NGS analysis.…”