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Background Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from caecal content samples taken from 24 chickens belonging to either a fast or a slower growing breed consuming either a vegetable-only diet or a diet containing fish meal. Results We utilise 1.6 T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species, and 42 novel genera. We compare our genomes to data from 9 European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome. Conclusions This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.

Background The chicken intestinal microbiota plays a large role in chicken health and productivity and a greater understanding of its development may lead to interventions to improve chicken nutrition, disease resistance and welfare. Results In this study we examine the duodenal, jejunal, ileal and caecal microbiota of chickens from day of hatch to 5 weeks of age (day 1, 3, 7, 14 and week 5). DNA was extracted from intestinal content samples and the V4 region of the 16S rRNA gene was amplified and sequenced. We identified significant differences in microbial community composition, diversity and richness between samples taken from different locations within the chicken intestinal tract. We also characterised the development of the microbiota at each intestinal site over time. Conclusions Our study builds upon existing literature to further characterise the development of the chicken intestinal microbiota.

Background The study explored the accuracy and biases of genomic selection in two commercial Pekin duck lines, focusing on their performance under real-world breeding practices. A dataset of 26 K duck records with phenotype and imputed genotype information (60 K chip) was analysed for growth, welfare, and primary feather length traits. Mixed linear models with relationship matrices from pedigree (BLUP) or markers (GBLUP) were used to estimate variance components and breeding values. We then assessed selection accuracies and biases to determine the most appropriate models. Results Results showed high imputation accuracies of 0.93 for line A and 0.92 for line D. Heritability estimates from pedigree were generally higher than those from genomic markers. For example, juvenile weight (JW) heritability ranged from 0.22 in line A and 0.25 in line D using markers, to 0.39 and 0.50, respectively, using the pedigree. Slaughter body weight (BW) had similar trends. Gait heritability was low (0.07) using markers in both lines, while breast muscle depth (BD) also had lower estimates (0.15–0.16). For line A, genomic prediction accuracies were higher with the G-matrix, especially for BW (r 2 =0.68-0.70) and JW with r 2 of 0.49. Estimates for gait and foot pad dermatitis (FPD) improved using the G-matrix at 0.58 vs. 0.24 and 0.68 vs. 0.44, respectively, compared to pedigree information. Similar improvements were found for line D, with BD estimates improving from 0.50 to 0.71 using the G-matrix. Line A showed minimal bias (0.01-0.19) with the G-matrix compared to 0.02-0.41 with the A-matrix; the highest bias was for JW. Line D had lower biases with the G-matrix (0.02-0.17) than in line A with markers, while higher biases were observed using pedigree (0.01-0.37). Conclusions These findings indicate that all traits were heritable with higher prediction accuracies and lower biases using GBLUP compared to BLUP. This study demonstrates the effectiveness of GBLUP in improving prediction accuracy and reducing bias in selection traits of Pekin ducks, particularly for traits with low heritability.

Average daily gain (ADG), body weight (BW), primary feather length (PRF) and breast depth (BD) are economically important traits in duck production, and understanding the genetic architecture of these traits remains limited. Genome-wide association studies (GWAS) can provide insight into the genetic mechanism underlying these traits. Increasing the power of GWAS by applying approaches such as genotype imputation can improve the ability to detect quantitative trait loci associations with polygenic traits. To increase the power of detecting marker-trait associations in this study, we also exploited imputed data and on a larger sample size. The objective of this study was to investigate marker-trait associations for ADG, BW, PRF and BD in ducks. First, we conducted univariate GWA analyses using chip data (hence medium density data) using 45 K autosomal SNPs and 1445 ducks from single breeding line. Second, we exploited imputed data with a larger sample size (13020) from the same line and performed univariate analyses. Comparison of SNP signals between the medium density and imputed data identified 63 common SNPs that were co-localized on chromosome 4. Several functional candidate genes such as PPARGC1A , LDB2 and LCORL were found within or close to the identified region. Indeed, the LCORL-NCAPG region has been reported in many mammalian species to be related to growth. Considering results from both analyses, current findings propose novel putative pleiotropic candidate quantitative trait loci (QTL) with the associated genes for the traits we analysed while identifying the most promising QTL region on chromosome 4.

To address the need for sensitive high-throughput assays to analyse avian innate and adaptive immune responses, we developed and validated a highly multiplexed qPCR 96.96 Fluidigm Dynamic Array to analyse the transcription of chicken immune-related genes. This microfluidic system permits the simultaneous analysis of expression of 96 transcripts in 96 samples in 6 nanolitre reactions and the 9,216 reactions are ready for interpretation immediately. A panel of 89 genes was selected from an RNA-seq analysis of the transcriptional response of chicken macrophages, dendritic cells and heterophils to agonists of innate immunity and from published transcriptome data. Assays were confirmed to be highly specific by amplicon sequencing and melting curve analysis and the reverse transcription and preamplification steps were optimised. The array was applied to RNA of various tissues from a commercial line of broiler chickens housed at two different levels of biosecurity. Gut-associated lymphoid tissues, bursa, spleen and peripheral blood leukocytes were isolated and transcript levels for immune-related genes were defined. The results identified blood cells as a potentially reliable indicator of immune responses among all the tissues tested with the highest number of genes significantly differentially transcribed between birds housed under varying biosecurity levels. Conventional qPCR analysis of three differentially transcribed genes confirmed the results from the multiplex qPCR array. A highly multiplexed qPCR-based platform for evaluation of chicken immune responses has been optimised and validated using samples from commercial chickens. Apart from applications in selective breeding programmes, the array could be used to analyse the complex interplay between the avian immune system and pathogens by including pathogen-specific probes, to screen vaccine responses, and as a predictive tool for immune robustness.

An amendment to this paper has been published and can be accessed via the original article.

Bangladeshi indigenous chicken varieties - Common Deshi, Hilly and Naked Neck are notable for their egg production, meat quality, extraordinary survivability and disease resistance. However, the potential to harness their unique genetic merits are being eroded by various factors, including crossbreeding. In-depth genomic studies have not been carried out on these breeds so far. To this end, blood samples and associated phenotypic metadata have been collected from local, unimproved birds sampled from 8 different locations across the country, and from Bangladesh Livestock Research Institute (BLRI)-improved chickens of the same mentioned breeds. Whole Genome Sequencing (WGS) of 96 selected samples, representing local and improved populations of each breed, has been carried out. Around 22 M high-quality SNPs have been identified, with 25% of these being novel variants previously undescribed in public databases. This data set will allow for genetic comparison between breeds, and between selected and unimproved birds, providing a resource for genomic selection in Bangladeshi breeding schemes to create more productive and resilient poultry stock.

Background Coccidiosis is a major contributor to losses in poultry production. With emerging constraints on the use of in-feed prophylactic anticoccidial drugs and the relatively high costs of effective vaccines, there are commercial incentives to breed chickens with greater resistance to this important production disease. To identify phenotypic biomarkers that are associated with the production impacts of coccidiosis, and to assess their covariance and heritability, 942 Cobb500 commercial broilers were subjected to a defined challenge with Eimeria tenella (Houghton). Three traits were measured: weight gain (WG) during the period of infection, caecal lesion score (CLS) post mortem , and the level of a serum biomarker of intestinal inflammation, i.e. circulating interleukin 10 (IL-10), measured at the height of the infection. Results Phenotypic analysis of the challenged chicken cohort revealed a significant positive correlation between CLS and IL-10, with significant negative correlations of both these traits with WG. Eigenanalysis of phenotypic covariances between measured traits revealed three distinct eigenvectors. Trait weightings of the first eigenvector, (EV1, eigenvalue = 59%), were biologically interpreted as representing a response of birds that were susceptible to infection, with low WG, high CLS and high IL-10. Similarly, the second eigenvector represented infection resilience/resistance (EV2, 22%; high WG, low CLS and high IL-10), and the third eigenvector tolerance (EV3, 19%; high WG, high CLS and low IL-10), respectively. Genome-wide association studies (GWAS) identified two SNPs that were associated with WG at the suggestive level. Conclusions Eigenanalysis separated the phenotypic impact of a defined challenge with E. tenella on WG, caecal inflammation/pathology, and production of IL-10 into three major eigenvectors, indicating that the susceptibility-resistance axis is not a single continuous quantitative trait. The SNPs identified by the GWAS for body weight were located in close proximity to two genes that are involved in innate immunity ( FAM96B and RRAD ).

Campylobacter is the leading cause of bacterial foodborne gastroenteritis worldwide. Handling or consumption of contaminated poultry meat is a key risk factor for human campylobacteriosis. One potential control strategy is to select poultry with increased resistance to Campylobacter . We associated high-density genome-wide genotypes (600K single nucleotide polymorphisms) of 3000 commercial broilers with Campylobacter load in their caeca. Trait heritability was modest but significant (h 2  = 0.11 ± 0.03). Results confirmed quantitative trait loci (QTL) on chromosomes 14 and 16 previously identified in inbred chicken lines, and detected two additional QTLs on chromosomes 19 and 26. RNA-Seq analysis of broilers at the extremes of colonisation phenotype identified differentially transcribed genes within the QTL on chromosome 16 and proximal to the major histocompatibility complex (MHC) locus. We identified strong cis -QTLs located within MHC suggesting the presence of cis -acting variation in MHC class I and II and BG genes. Pathway and network analyses implicated cooperative functional pathways and networks in colonisation, including those related to antigen presentation, innate and adaptive immune responses, calcium, and renin–angiotensin signalling. While co-selection for enhanced resistance and other breeding goals is feasible, the frequency of resistance-associated alleles was high in the population studied and non-genetic factors significantly influenced Campylobacter colonisation.

Background The importance of poultry as a global source of protein underpins the chicken genome and associated SNP data as key tools in selecting and breeding healthy robust birds with improved disease resistance. SNPs affecting host peptides involved in the innate defences tend to be rare, but three non-synonymous SNPs in the avian β-defensin (AvBD1) gene encoding the variant peptides NYH, SSY and NYY were identified that segregated specifically to three lines of commercial broiler chickens Line X (LX), Line Y(LY) and Line Z. The impacts of such amino acid changes on peptide antimicrobial properties were analysed in vitro and described in relation to the caecal microbiota and gut health of LX and LY birds. Results Time-kill and radial immune diffusion assays indicated all three peptides to have antimicrobial properties against gram negative and positive bacteria with a hierarchy of NYH > SSY > NYY. Calcein leakage assays supported AvBD1 NYH as the most potent membrane permeabilising agent although no significant differences in secondary structure were identified to explain this. However, distinct claw regions, identified by 3D modelling and proposed to play a key role in microbial membrane attachment, and permeation, were more distinct in the NYH model. In vivo AvBD1 synthesis was detected in the bird gut epithelia. Analyses of the caecal gut microbiota of young day 4 birds suggested trends in Lactobacilli sp. colonisation at days 4 (9% LX vs × 30% LY) and 28 (20% LX vs 12% LY) respectively, but these were not statistically significant ( P  > 0.05). Conclusion Amino acid changes altering the killing capacity of the AvBD1 peptide were associated with two different bird lines, but such changes did not impact significantly on caecal gut microbiota.