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 census 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. 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.

Background The prevalence of sexually transmitted infections (STIs) in sub-Saharan Africa is poorly described. We aimed to determine the prevalence of five curable STIs (Chlamydia trachomatis [CT], Neisseria gonorrhoeae [NG], Trichomonas vaginalis [TV], Mycoplasma genitalium [MG], Treponema pallidum [TP]) in a sample of Gambian women from the general population. Methods Archived specimens from 420 women aged 15 − 69 years living in The Gambia enrolled in a clinical trial of human papilloma virus vaccine schedules were tested in this study. Urine samples were tested for CT, NG, TV and MG using a commercially available, open-platform multiplex PCR kit. A fragment of the ompA gene was amplified from CT-positive samples and sequenced. Serum samples were tested for TP using the Chembio DPP Syphilis Screen and Confirm test. Results Overall, 41/420 (9.8%) women had at least one STI. 32 (7.6%), 9 (2.1%), 1 (0.2%), 1 (0.2%) and 0 (0.0%) were infected with TV, CT, NG, MG and TP, respectively. ompA gene sequence was available from five CT infections: four were genovar D and one was genovar G. Conclusions STIs are endemic in The Gambia. Monitoring systems should be established.

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