Jarju, Sheikh

Publications (1)

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

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