A Genomic Blueprint of the Chicken Gut Microbiome

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 bacterial isolates from faeces to deliver 282 whole genome sequences, incorporating 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.

Metagenome-based comparisons of decay rates and host-specificity of fecal microbial communities for improved microbial source tracking

“…Thus, it will be important to determine if these MAGs are present in animals from other herds across broader geographical regions. Many recent studies have made considerable effort to sequence metagenomes and/or assemble MAGs from cow rumen (53)(54)(55) as well a pig (56,57) and chicken guts (58). However, this information has not yet been synthesized together for MST marker development.…”

The Next Million Names for Archaea and Bacteria

“…Let us say we wish to explore a biome-specific generic namespace defined by combinations of three terms (Figure 1, Key Figure). If we select ten roots to be deployed in each of the initial, middle, and final positions, then it becomes possible to create, from just 30 roots, ten-times-ten-timesten = a thousand names with little effortan approach we have already used to create names for several hundred new genera from the chicken gut microbiome [25].…”

Spotlight on the avian gut microbiome: fresh opportunities in discovery

“…In particular, analysis of DNA extracted from faecal or caecal samples en masse ("shotgun metagenomics") (Sergeant et al, 2014;Glendinning et al, 2020) has allowed us to overcome the biases and bottlenecks associated with culture. Through the use of both culture-based and sequence-based strategies, we have recently uncovered vast genetic, functional and taxonomic diversity in this setting (Glendinning et al, 2020;Gilroy et al, 2021), documenting millions of genes, thousands of bacterial genomes and hundreds of new species.…”

“…Our own microbiome research has opened up new horizons in discovering, documenting and characterizing a microbial parts list for the chicken gut (Gilroy et al, 2021). The resulting datasets greatly 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.…”