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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. We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all ( = 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 , including the newly named species . 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.

We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method performance was demonstrated by sequencing 2 plates containing 95 and 59 SARS-CoV-2 genomes on nanopore and Illumina platforms and comparing to the ARTIC LoCost nanopore method. Of the 154 samples sequenced using all 3 methods, ≥ 90% genome coverage was obtained for 64.3% using ARTIC LoCost, 71.4% using CoronaHiT-ONT and 76.6% using CoronaHiT-Illumina, with almost identical clustering on a maximum likelihood tree. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally.

The horse plays crucial roles across the globe, including in horseracing, as a working and companion animal and as a food animal. The horse hindgut microbiome makes a key contribution in turning a high fibre diet into body mass and horsepower. However, despite its importance, the horse hindgut microbiome remains largely undefined. Here, we applied culture-independent shotgun metagenomics to thoroughbred equine faecal samples to deliver novel insights into this complex microbial community. We performed metagenomic sequencing on five equine faecal samples to construct 123 high- or medium-quality metagenome-assembled genomes from Bacteria and Archaea. In addition, we recovered nearly 200 bacteriophage genomes. We document surprising taxonomic diversity, encompassing dozens of novel or unnamed bacterial genera and species, to which we have assigned new names. Many of these genera are conserved across a range of mammalian gut microbiomes. Our metagenomic analyses provide new insights into the bacterial, archaeal and bacteriophage components of the horse gut microbiome. The resulting datasets provide a key resource for future high-resolution taxonomic and functional studies on the equine gut microbiome.

Background The canine microbiome is a vastly understudied area relative to the importance of dogs in society, particularly given the potential importance of the microbiome in veterinary medicine. This has led to a large knowledge gap in the basic taxonomy and functions of the canine gut microbiome and an overreliance on human databases for canine-specific research. Using a broad sample set, long read sequencing, short read sequencing, and metagenomic assembly approaches, we have produced the most comprehensive microbiome resource in all companion animal research. Results Here, we describe the recovery of 240 core species that account for > 80% of the canine gut microbiome when tested on an independent validation dataset. We uncovered > 900 new canine-specific strains, 89 novel species, and 10 novel genera, providing a dramatic increase in previous knowledge of the canine microbiome and allowing for mapping rates of up to 95%, a 70% increase on historic mapping rates of ~ 25% using publicly available resources. Through detailed annotation of function, we demonstrate the potential importance of the novel species and genera to health and nutrition and provide evidence of new canine-adapted strains of existing genera and species previously unknown to inhabit canines that provide important metabolic function to the canine host. We discovered the canine microbiome has an expansive ability to metabolize carbohydrates, providing insight into how canines process diverse carbohydrates given their known limited host genomic potential. We uncovered a range of species with abilities to produce butyrate, propionate, and vitamins, highlighting the importance of the canine microbiome to host nutrition. We describe two novel Peptacetobacter species that could regulate host bile acid metabolism, an important finding in the context of chronic GI disease in pets. We demonstrated all new species and genera had no known virulence, suggesting they are commensal and, finally, provided a baseline for antimicrobial resistance in the microbiota species of healthy pets. Conclusions This work gives entirely new perspectives on the functional capabilities of the canine gut microbiome, suggesting the canine microbiome is distinct, presumably having evolved to its host, diet, and environment over several millennia. DuMW3s1Cbj6t_NkpoVSPVB Video Abstract

Over recent decades, Salmonella infection research has predominantly relied on murine infection models. However, in many cases the infection phenotypes of Salmonella pathovars in mice do not recapitulate human disease. For example, Salmonella Typhimurium ST313 is associated with enhanced invasive infection of immunocompromised people in Africa, but infection of mice and other animal models with ST313 have not consistently reproduced this invasive phenotype. The introduction of alternative infection models could help to improve the quality and reproducibility of pathogenesis research by facilitating larger-scale experiments. To investigate the virulence of S. Typhimurium ST313 in comparison with ST19, a combination of avian and insect disease models were used. We performed experimental infections in five lines of inbred and one line of outbred chickens, as well as in the alternative chick embryo and Galleria mellonella wax moth larvae models. This extensive set of experiments identified broadly similar patterns of disease caused by the African and global pathovariants of Salmonella Typhimurium in the chicken, the chicken embryo and insect models. A comprehensive analysis of all the chicken infection experiments revealed that the African ST313 isolate D23580 had a subtle phenotype of reduced levels of organ colonisation in inbred chickens, relative to ST19 strain 4/74. ST313 isolate D23580 also caused reduced mortality in chicken embryos and insect larvae, when compared with ST19 4/74. We conclude that these three infection models do not reproduce the characteristics of the systemic disease caused by S. Typhimurium ST313 in humans.

The genus Escherichia has been extensively studied and it is known to encompass a range of commensal and pathogenic bacteria that primarily inhabit the gastrointestinal tracts of warm-blooded vertebrates. However, the presence of E. coli as a model organism and potential pathogen has diverted attention away from commensal strains and other species in the genus. To investigate the diversity of Escherichia in healthy chickens, we collected fecal samples from antibiotic-free Lohmann Brown layer hens and determined the genome sequences of 100 isolates, 81 of which were indistinguishable at the HC0 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing scheme. Despite initial selection on CHROMagar Orientation medium, which is considered selective for E. coli , in silico phylotyping and core genome single nucleotide polymorphism analysis revealed the presence of at least one representative of all major clades of Escherichia , except for E. albertii, Shigella , and E. coli phylogroup B2 and cryptic clade I. The most frequent phylogenomic groups were E. coli phylogroups A and B1 and E. ruysiae (clades III and IV). We compiled a collection of reference strains isolated from avian sources (predominantly chicken), representing every Escherichia phylogroup and species, and used it to confirm the phylogeny and diversity of our isolates. Overall, the isolates carried low numbers of the virulence and antibiotic resistance genes typically seen in avian pathogenic E. coli . Notably, the clades not recovered are ones that have been most strongly associated with virulence by other studies.

Complex carbohydrates that escape small intestinal digestion, are broken down in the large intestine by enzymes encoded by the gut microbiome. This is a symbiotic relationship between microbes and host, resulting in metabolic products that influence host health and are exploited by other microbes. However, the role of carbohydrate structure in directing microbiota community composition and the succession of carbohydrate-degrading microbes, is not fully understood. In this study we evaluate species-level compositional variation within a single microbiome in response to six structurally distinct carbohydrates in a controlled model gut using hybrid metagenome assemblies. We identified 509 high-quality metagenome-assembled genomes (MAGs) belonging to ten bacterial classes and 28 bacterial families. Bacterial species identified as carrying genes encoding starch binding modules increased in abundance in response to starches. The use of hybrid metagenomics has allowed identification of several uncultured species with the functional potential to degrade starch substrates for future study. Longitudinal hybrid metagenomic analyses of a human stool sample reveal compositional and functional variation in response to six structurally-distinct carbohydrates, providing insight into how gut bacteria utilize various carbohydrate sources.

Campylobacter jejuni is the leading cause of foodborne bacterial gastroenteritis with contaminated poultry meat its main source. Control of C. jejuni is a priority for the poultry industry but no vaccines are available and their development hampered by poor understanding of the immunobiology of C. jejuni infection. Here we show the functional role of B lymphocytes in response to C. jejuni in the chicken through depletion of the B lymphocyte population (bursectomy) followed by challenge. B lymphocyte depletion has little effect on bacterial numbers in the ceca, the main site of colonisation, where C. jejuni persist to beyond commercial slaughter age, but reduces clearance from the small intestine. In longer-term experiments we show antibody leads to reduction in C. jeuni numbers in the ceca by nine weeks post infection. Whilst we did not examine any protective role to re-challenge, it illustrates the difficulty in producing a vaccine in a young, immunologically naïve host. We believe this is first study of functional immunity to C. jejuni in chicken and shows antibody is ineffective in clearing C. jejuni from the ceca within the production lifetime of chickens, although is involved in clearance from the small intestine and longer-term clearance from the ceca.

Campylobacter jejuni is the most frequent cause of bacterial foodborne gastroenteritis worldwide and is thought to affect ~ 600, 000 people in the UK each year alone. The preparation and consumption of poultry meat remains the single source of human Campylobacter infection. With over 60 % of UK retail chicken carcasses showing Campylobacter contamination, the poultry sector represents a crucial reservoir for human disease. Having been previously considered a commensal within avian species, infection biology of C. jejuni within the broiler chicken shows limited understanding. Despite numerous efforts to develop both on-farm and post-slaughter controls, these have all proven to be of limited efficacy. Therefore, an improved understanding of the infection biology of Campylobacter in the chicken and effective control methods are a priority Here we used in vivo experimental methods to develop our understanding of the complex infection dynamics and host-microbe interactions associated with prolonged Campylobacter infection within a commonly used broiler chicken breed. Sampled between 2 & 28 days post-infection (d.p.i), bacteriological analysis revealed rapid C. jejuni colonisation of the chicken gastrointestinal tract, persisting at a high burden within the caecal crypts once established. While infrequent, evidence of systemic spread of C. jejuni to liver and splenic tissues was observed in all experimental trials, further confirming the invasive ability within the chicken. Early C. jejuni colonisation was associated with early upregulation of pro-inflammatory and Th-17 immune mediators (IL-1β, IL-6, IL17A and CXCLi2) (p < 0.05) caecal and caecal tonsil tissue. Prolonged C. jejuni colonisation from 7 d.p.i onward was instead associated with regulatory immune mediators, IL-10 and TGFβ4 (p < 0.05). Modulation of the intestinal microbiome has been proposed as a potential control strategy for foodborne bacterial pathogens within poultry production, particularly as commercial chickens are reared in hatcheries with no maternal contact to develop an early or pioneer microbiome. We examined whether the at-hatch delivery of adult chicken caecal microflora (CMT) would lead to a more natural ‘avian’ microbiota which, in-turn, could drive an improvement in chicken gut health and reduce susceptibility to C. jejuni infection. Delivery of 0.1 - 0.2 ml CMT preparation (derived from 7-week old broiler chickens) within 4 hours post-hatch subsequently resulted in reduced within-flock transmission of C. jejuni and a reduced caecal C. jejuni burden (p < 0.05) following experimental infection compared to control birds. This response was consistently reproducible and sustained until commercial slaughter age. Compared to a commercial competitive exclusion microflora preparation (Aviguard® ), CMT administration was significantly more protective against C. jejuni colonisation of the caeca (p < 0.05). 16S rRNA Illumina MiSEQ analysis showed caecal content of birds treated with CMT had higher relative abundance of Firmicutestaxa – namely Ruminococcaceae (p < 0.05) compared to untreated control and Aviguard® treated birds. Caecal content of CMT treated chicks showed higher community richness compared to caecal content of both control (p < 0.001) and Aviguard® treated chicks (p < 0.001). These findings indicate that a novel, at-hatch transplantation of an adult chicken microbiota might prematurely drive successional development of the chick microbiota and reduce chicken susceptibility to experimental C. jejuni infection more effectively than a commercial competitive exclusion product.

The real problems, needs and opportunities of urban neighborhoods are not being served by conventional models of urban planning and sustainable development. The city of New Haven, Connecticut will be studied to develop a framework for planning and design of the public realm (public space/place/landscape) which addresses urban neighborhood sustainability through a social lens, using a mixed-methods, transdisciplinarity research model. Geospatial data on social capital and cultural vitality indicators will be integrated with other sustainability indicators to create a quantitative analysis component. Development of a participatory design process to foster social bonding, creativity and sustainability inquiry will comprise a qualitative component for the framework.