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

Gilroy et al. (2021). PeerJ 9
Names (94)
“Mediterraneibacter excrementigallinarum” “Ruthenibacterium merdavium” “Gemmiger stercoravium” “Eisenbergiella intestinipullorum” “Merdibacter merdavium” “Enterocloster excrementipullorum” “Borkfalkia stercoripullorum” “Gemmiger stercoripullorum” “Merdibacter merdigallinarum” “Intestinimonas stercoravium” “Limosilactobacillus intestinipullorum” “Mediterraneibacter pullistercoris” “Faecalibacterium gallistercoris” “Borkfalkia excrementigallinarum” “Mediterraneibacter stercoripullorum” “Anaerotignum merdipullorum” “Fusicatenibacter merdavium” “Anaerostipes excrementavium” “Blautia pullistercoris” “Hungatella pullicola” “Borkfalkia faecipullorum” “Acetatifactor stercoripullorum” “Mediterraneibacter vanvlietii” “Eisenbergiella stercoravium” “Butyricicoccus avistercoris” “Blautia stercorigallinarum” “Acutalibacter stercorigallinarum” “Mediterraneibacter excrementavium” “Corynebacterium faecigallinarum” “Phocaeicola excrementigallinarum” “Blautia merdavium” “Anaerostipes avistercoris” “Dietzia intestinigallinarum” “Mediterraneibacter faecigallinarum” “Mediterraneibacter faecipullorum” “Dietzia intestinipullorum” “Alistipes stercoravium” “Eisenbergiella merdavium” “Ligilactobacillus avistercoris” “Eisenbergiella merdigallinarum” “Nosocomiicoccus stercorigallinarum” “Mailhella merdavium” “Fournierella excrementigallinarum” “Fournierella merdavium” “Desulfovibrio gallistercoris” “Blautia merdipullorum” “Phocaeicola faecigallinarum” “Alistipes avicola” “Bariatricus faecipullorum” “Desulfovibrio intestinavium” “Brachybacterium merdavium” “Brevibacterium intestinavium” “Agathobaculum intestinipullorum” “Limosilactobacillus excrementigallinarum” “Mediterraneibacter merdigallinarum” “Fournierella merdigallinarum” “Mediterraneibacter pullicola” “Mediterraneibacter merdipullorum” “Microbacterium stercoravium” “Collinsella stercoripullorum” “Ligilactobacillus excrementavium” “Mucispirillum faecigallinarum” “Janibacter merdipullorum” “Lactobacillus pullistercoris” “Atopostipes pullistercoris” “Gemmiger excrementavium” “Fournierella merdipullorum” “Ruania gallistercoris” “Tidjanibacter faecipullorum” “Companilactobacillus pullicola” “Rothia avicola” “Rubneribacter avistercoris” “Sphingobacterium stercorigallinarum” “Intestinimonas merdavium” “Luteimonas excrementigallinarum” “Alistipes intestinigallinarum” “Tetragenococcus pullicola” “Eisenbergiella pullistercoris” “Agathobaculum merdavium” “Evtepia faecavium” “Barnesiella excrementavium” “Acutalibacter pullistercoris” “Anaerofilum excrementigallinarum” “Evtepia faecigallinarum” “Gemmiger excrementipullorum” “Anaerobiospirillum pullistercoris” “Acinetobacter avistercoris” “Limosilactobacillus merdigallinarum” “Desulfovibrio intestinigallinarum” “Blautia stercoravium” “Barnesiella excrementigallinarum” “Gemmiger faecavium” “Alectryobacillus” “Alectryobacillus merdavium”
General Agricultural and Biological Sciences General Biochemistry, Genetics and Molecular Biology General Medicine General Neuroscience
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.
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