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

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

SARS-CoV-2 variants of interest and concern naming scheme conducive for global discourse

A group convened and led by the Virus Evolution Working Group of the World Health Organization reports on its deliberations and announces a naming scheme that will enable clear communication about SARS-CoV-2 variants of interest and concern.Molecular basis of virus replication, viral pathogenesis and antiviral strategie

Detection and characterisation of diphtheria toxin genes and insertion sequences by PCR and other molecular techniques

SIGLEAvailable from British Library Document Supply Centre-DSC:DX200958 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

An investigation into the links between stationary phase and virulence in Salmonella enterica entercial serovar typhimurium

SIGLEAvailable from British Library Document Supply Centre-DSC:DXN025825 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

Cutaneous and pharyngeal diphtheria imported from the Indian subcontinent.

We report the case of a 32-year-old woman who presented upon returning from India with cutaneous ulcers on the feet and pharyngitis. Microbiological testing showed the causative organism to be a toxigenic strain of Corynebacterium diphtheriae. She was treated successfully with penicillin and diphtheria antitoxin. This case emphasises the importance of maintaining a high index of suspicion for such rare but significant infectious diseases

High-throughput whole-genome sequencing to dissect the epidemiology of acinetobacter baumannii isolates from a hospital outbreak

Shared care of military and civilian patients has resulted in transmission of multidrug-resistant Acinetobacter baumannii (MDR-Aci) from military casualties to civilians. Current typing technologies have been useful in revealing relationships between isolates of A. baumannii but they are unable to resolve differences between closely related isolates from small-scale outbreaks, where chains of transmission are often unclear. In a recent hospital outbreak in Birmingham, six patients were colonised with MDR-Aci isolates indistinguishable using standard techniques. We used whole-genome sequencing to identify single nucleotide polymorphisms in these isolates, allowing us to discriminate between alternative epidemiological hypotheses in this setting