Effects of anti-coccidial vaccination and exogenous enzymes on chicken growth performance and gut health

Gut health is the relationship between the host, gut microbes and diet. Therefore, comprehensive analyses of the host immune system, microbiota and diets in the same setting are required in order to study gut health. Correlations between the host immune system and the gut microbiota could provide a better understanding of the relationship between host and microbes. Knowledge of the relationships between the intestinal immune system and microbiota could help producers improve poultry health and nutrient utilisation. Application of this knowledge could result in better poultry growth performance, animal welfare and reduced environmental impact. Two by two factorial arrangement study was conducted using Ross 308 broiler chickens. Anti-coccidial vaccination against Eimeria protozoa was used as a factor to create gut-damaged chickens. Combination of protease, xylanase and beta-glucanase enzymes was used as a dietary intervention factor. Chicken growth performance was significantly affected by the vaccination while enzymes supplement significantly improved the feed conversion ratio. Although coccidiosis lesions were observed in non-vaccinated chickens at 24-day-old, the feed efficiency of non-vaccinated chickens still outperformed the vaccinated chickens at this period. While at 35 days of age, vaccinated chickens showed compensatory growth with significantly better growth performance than non-vaccinated chickens. Therefore, samples for correlation analysis were selected from 24-day-old rather than 35-day-old chickens. Using 16S rRNA metabarcoding analysis, the abundances of eleven bacterial genera at the ileum of 24-day-old chicken were significantly affected by the vaccination where two bacterial genera were significantly affected in the caecum. Although the enzymes supplement did not significantly affect the microbiota population at both ileum and caecum from 16S rRNA metabarcoding analysis, functional analysis using shotgun metagenomics and Carbohydrate Active enzymes database (CAzy) showed significant alteration by the enzymes supplement. From transcriptomic analysis, vaccination significantly affected the expression of 96 and 46 genes at the ileum and caecum respectively. In contrast, 4 and 3 genes were differentially expressed between the enzymes and non-enzymes supplement chicken at the ileum and caecum respectively. At both ileum and caecum, several immune-related genes were up-regulated while multiple absorption-related genes were down-regulated in vaccinated chicken. Interestingly, with more differentially expressed genes at the ileum than the caecum, no Gene Ontology (GO) term was significantly enriched at the ileum when compared between vaccinated and non-vaccinated chicken. Correlation between gut microbiota and gene expression using Weighted Gene Co-expression Network Analysis (WGCNA) showed multiple significant correlations between gene clusters and bacterial taxa. Using differentially expressed gene results from the RNA-seq analysis, 84 and 191 significant correlations were identified at ileum and caecum respectively. In conclusion, anti-coccidial vaccination had a significant impact on chicken growth performance, gut microbiota and intestinal immune response. Alteration of the nutrition using exogenous enzymes improved feed efficiency with minor impact on the gut microbiota and host response. Correlation between gut microbiota and intestinal gene expression were identified. These bacteria and genes could be used as potential markers for gut health however, further investigation using these findings is required

Genetic characterization of avian influenza subtype H4N6 and H4N9 from live bird market, Thailand

A one year active surveillance program for influenza A viruses among avian species in a live-bird market (LBM) in Bangkok, Thailand was conducted in 2009. Out of 970 samples collected, influenza A virus subtypes H4N6 (n = 2) and H4N9 (n = 1) were isolated from healthy Muscovy ducks. All three viruses were characterized by whole genome sequencing with subsequent phylogenetic analysis and genetic comparison. Phylogenetic analysis of all eight viral genes showed that the viruses clustered in the Eurasian lineage of influenza A viruses. Genetic analysis showed that H4N6 and H4N9 viruses display low pathogenic avian influenza characteristics. The HA cleavage site and receptor binding sites were conserved and resembled to LPAI viruses. This study is the first to report isolation of H4N6 and H4N9 viruses from birds in LBM in Thailand and shows the genetic diversity of the viruses circulating in the LBM. In addition, co-infection of H4N6 and H4N9 in the same Muscovy duck was observed

Genetic characterization of 2008 reassortant influenza A virus (H5N1), Thailand

In January and November 2008, outbreaks of avian influenza have been reported in 4 provinces of Thailand. Eight Influenza A H5N1 viruses were recovered from these 2008 AI outbreaks and comprehensively characterized and analyzed for nucleotide identity, genetic relatedness, virulence determinants, and possible sites of reassortment. The results show that the 2008 H5N1 viruses displayed genetic drift characteristics (less than 3% genetic differences), as commonly found in influenza A viruses. Based on phylogenetic analysis, clade 1 viruses in Thailand were divided into 3 distinct branches (subclades 1, 1.1 and 1.2). Six out of 8 H5N1 isolates have been identified as reassorted H5N1 viruses, while other isolates belong to an original H5N1 clade. These viruses have undergone inter-lineage reassortment between subclades 1.1 and 1.2 and thus represent new reassorted 2008 H5N1 viruses. The reassorted viruses have acquired gene segments from H5N1, subclade 1.1 (PA, HA, NP and M) and subclade 1.2 (PB2, PB1, NA and NS) in Thailand. Bootscan analysis of concatenated whole genome sequences of the 2008 H5N1 viruses supported the reassortment sites between subclade 1.1 and 1.2 viruses. Based on estimating of the time of the most recent common ancestors of the 2008 H5N1 viruses, the potential point of genetic reassortment of the viruses could be traced back to 2006. Genetic analysis of the 2008 H5N1 viruses has shown that most virulence determinants in all 8 genes of the viruses have remained unchanged. In summary, two predominant H5N1 lineages were circulating in 2008. The original CUK2-like lineage mainly circulated in central Thailand and the reassorted lineage (subclades 1.1 and 1.2) predominantly circulated in lower-north Thailand. To prevent new reassortment, emphasis should be put on prevention of H5N1 viruses circulating in high risk areas. In addition, surveillance and whole genome sequencing of H5N1 viruses should be routinely performed for monitoring the genetic drift of the virus and new reassorted strains, especially in light of potential reassortment between avian and mammalian H5N1 viruses

Role of caecal microbiota in the differential resistance of inbred chicken lines to colonization by Campylobacter jejuni

Campylobacter is the leading foodborne bacterial diarrhoeal illness in many countries, with up to 80 % of human cases attributed to the avian reservoir. The only control strategies currently available are stringent on-farm biosecurity and carcass treatments. Heritable differences in the resistance of chicken lines to Campylobacter colonisation have been reported and resistance-associated quantitative trait loci are emerging, albeit their impact on colonization appears modest. Recent studies indicated a protective role of the microbiota against colonization by Campylobacter in chickens. Furthermore, in murine models, differences in resistance to bacterial infections can be partially transferred between lines by transplantation of gut microbiota. In this study, we investigated whether heritable differences in colonization of inbred chicken lines by Campylobacter jejuni are associated with differences in caecal microbiota. We performed homologous and heterologous caecal microbiota transplants between line 61 (resistant) and line N (susceptible), by orally administering caecal contents collected from 3-week-old donors to day-of-hatch chicks. Recipient birds were challenged (day 21) with C. jejuni 11168H. In birds given homologous microbiota, the differential resistance of lines to C. jejuni colonization was reproduced. Contrary to our hypothesis, transfer of caecal microbiota from line 61 to line N significantly increased C. jejuni colonization. No significant difference in the overall composition of the caecal microbial communities of the two lines was identified, albeit line-specific differences for specific operational taxonomic units were identified. Our data suggest that while heritable differences in avian resistance to Campylobacter colonization exist, these are not explained by significant variation in the caecal microbiota