Genetic control of<i>Campylobacter</i>colonisation in broiler chickens: genomic and transcriptomic characterisation

Psifidi, Androniki; Kranis, Andreas; Rothwell, Lisa; Bremner, Abi; Russell, Kay; Robledo, Diego; Bush, Stephen J.; Fife, Mark; Hocking, Paul; Banos, Georgios; Hume, David; Kaufman, Jim; Bailey, Richard; Avendaño, S.; Watson, Kellie; Kaiser, Pete; Stevens, Mark P.

doi:10.1101/2020.04.14.040832

Cited by 3 publications

(7 citation statements)

References 85 publications

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“…Although we recognise that microbial diversity will increase naturally from day 7 to day 30, based on our data, Campylobacter is associated with an increasing diversity. Broiler genetics is known to impact microbial diversity [47,48] and this may explain why in our study the environmental pressure was significantly impacted positively by the presence of Campylobacter. Here, the environmental influence may be the chicken host genetics influencing microbial community structure.…”

Section: Discussionmentioning

confidence: 74%

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter

et al. 2020

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Background The factors affecting host-pathogen ecology in terms of the microbiome remain poorly studied. Chickens are a key source of protein with gut health heavily dependent on the complex microbiome which has key roles in nutrient assimilation and vitamin and amino acid biosynthesis. The chicken gut microbiome may be influenced by extrinsic production system parameters such as Placement Birds/m2 (stocking density), feed type and additives. Such parameters, in addition to on-farm biosecurity may influence performance and also pathogenic bacterial numbers such as Campylobacter. In this study, three different production systems ‘Normal’ (N), ‘Higher Welfare’ (HW) and ‘Omega-3 Higher Welfare’ (O) were investigated in an industrial farm environment at day 7 and day 30 with a range of extrinsic parameters correlating performance with microbial dynamics and Campylobacter presence. Results Our data identified production system N as significantly dissimilar from production systems HW and O when comparing the prevalence of genera. An increase in Placement Birds/m2 density led to a decrease in environmental pressure influencing the microbial community structure. Prevalence of genera, such as Eisenbergiella within HW and O, and likewise Alistipes within N were representative. These genera have roles directly relating to energy metabolism, amino acid, nucleotide and short chain fatty acid (SCFA) utilisation. Thus, an association exists between consistent and differentiating parameters of the production systems that affect feed utilisation, leading to competitive exclusion of genera based on competition for nutrients and other factors. Campylobacter was identified within specific production system and presence was linked with the increased diversity and increased environmental pressure on microbial community structure. Addition of Omega-3 though did alter prevalence of specific genera, in our analysis did not differentiate itself from HW production system. However, Omega-3 was linked with a positive impact on weight gain. Conclusions Overall, our results show that microbial communities in different industrial production systems are deterministic in elucidating the underlying biological confounders, and these recommendations are transferable to farm practices and diet manipulation leading to improved performance and better intervention strategies against Campylobacter within the food chain.

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Section: Discussionmentioning

confidence: 74%

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter

et al. 2020

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show abstract

“…Campylobacter is associated with an increasing diversity. Broiler genetics is known to impact microbial diversity [47,48] and this may explain why in our study the environmental pressure was significantly impacted positively by the presence of Campylobacter. Here the environmental influence may be the chicken host genetics influencing microbial community structure.…”

Section: Discussionmentioning

confidence: 74%

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduceCampylobacter

McKenna

Ijaz

Kelly

et al. 2020

Preprint

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BackgroundThe factors affecting host-pathogen ecology in terms of the microbiome remain poorly studied. Chickens are a key source of protein with gut health heavily dependent on the complex microbiome which has key roles in nutrient assimilation and vitamin and amino acid biosynthesis. The chicken gut microbiome may be influenced by extrinsic production system parameters such as Placement Birds/m2 (stocking density), feed type and additives. Such parameters, in addition to on-farm biosecurity may influence performance and also pathogenic bacterial numbers such as Campylobacter. In this study, three different production systems ‘Normal’ (N), ‘Higher Welfare’ (HW) and ‘Omega-3 Higher Welfare’ (O) were investigated “in a natural environment” at day 7 and day 30 with a range of extrinsic parameters assessing performance in correlation with microbial dynamics and Campylobacter presence.ResultsOur data identified production system N as significantly dissimilar from production systems HW and O when comparing the prevalence of genera. An increase in Placement Birds/m2 density led to a decrease in environmental pressure influencing the microbial community structure. Prevalence of genera such as Eisenbergiella within HW and O, and likewise Alistipes within N were representative. These genera have roles directly relating to energy metabolism, amino acid, nucleotide and short chain fatty acid (SCFA) utilisation. Thus, an association exists between consistent and differentiating parameters of the production systems, that affect feed utilisation, advance our knowledge of mechanistic underpinnings, leading to competitive exclusion of genera based on competition for nutrients and other factors. Campylobacter was identified within specific production system and presence was linked with the increased diversity and increased environmental pressure on microbial community structure. Addition of Omega-3 though did alter prevalence of specific genera, in our analysis did not differentiate itself from HW production system. However, Omega-3 was linked with a positive impact on weight gain.ConclusionsOverall, our results show that microbial communities in different industrial production systems are deterministic in elucidating the underlying biological confounders, and these recommendations are transferable to farm practices and diet manipulation leading to improved performance and better intervention strategies against Campylobacter within the food chain.Graphical Abstract

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“…Differences exist in the levels of colonisation across and within commercial broiler lines [13,14] and these have been associated with variation in the transcriptome of the caeca [14][15][16] and spleen [17]. Genome-wide association studies in a commercial broiler population have indicated that resistance to caecal C. jejuni colonisation is under moderate genetic control [14]. However, heritable differences in resistance have been associated with quantitative trait loci (QTL) [14,18], and the transcription of genes related to immunity [14,19].…”

Section: Introductionmentioning

confidence: 99%

“…One option to achieve this is to improve the intrinsic resistance of chickens to Campylobacter colonisation. Differences exist in the levels of colonisation across and within commercial broiler lines [13,14] and these have been associated with variation in the transcriptome of the caeca [14][15][16] and spleen [17]. Genome-wide association studies in a commercial broiler population have indicated that resistance to caecal C. jejuni colonisation is under moderate genetic control [14].…”

Section: Introductionmentioning

confidence: 99%

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Transcriptomic analysis of caecal tissue in inbred chicken lines that exhibit heritable differences in resistance to Campylobacter jejuni

Russell

Smith

Bremner

et al. 2021

Preprint

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Background Campylobacter jejuni is the leading cause of bacterial gastroenteritis in humans and the handling or consumption of contaminated poultry meat is a key source of infection. Selective breeding of poultry that exhibit elevated resistance to Campylobacter is an attractive control strategy. Here we studied the global transcriptional response of inbred chicken lines that differ in resistance to C. jejuni colonisation at a key site of bacterial persistence. Results Three-week-old chickens of line 61 and N were inoculated orally with C. jejuni strain M1 and caecal contents and tonsils were sampled at 1 and 5 days post-infection. Caecal colonisation was significantly lower in line 61 compared to line N at 1 day post-infection, but not 5 days post-infection. RNA-Seq analysis of caecal tonsils of both lines revealed a limited response to C. jejuni infection compared to age-matched uninfected controls. In line N at days 1 and 5 post-infection, just 8 and 3 differentially expressed genes (DEGs) were detected (fold-change > 2 and false-discovery rate of < 0.05) relative to uninfected controls, respectively. In the relatively resistant line 61, a broader response to C. jejuni was observed, with 69 DEGs relating to immune regulation, cell signalling and metabolism at 1 day post-infection. However, by day 5 post-infection, no DEGs were detected. By far, the greatest number of DEGs were between uninfected birds of the two lines implying that differential resistance to C. jejuni is intrinsic. Of these genes, several Major Histocompatibility Complex class I-related genes (MHCIA1, MHCBL2 and MHCIY) and antimicrobial peptides (MUC2, AvBD10 and GZMA) were expressed to a greater extent in line N. Two genes within quantitative trait loci associated with C. jejuni colonisation were also more highly expressed in line N (ASIC4 and BZFP2). Quantitative reverse-transcriptase PCR analysis of a subset of transcripts confirmed the RNA-Seq results. Conclusions Our data indicate a limited transcriptional response in the caecal tonsils of inbred chickens to intestinal colonisation by Campylobacter but identify a large number of differentially transcribed genes between lines 61 and N that may underlie variation in heritable resistance to C. jejuni.

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Genetic control ofCampylobactercolonisation in broiler chickens: genomic and transcriptomic characterisation

Cited by 3 publications

References 85 publications

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduceCampylobacter

Transcriptomic analysis of caecal tissue in inbred chicken lines that exhibit heritable differences in resistance to Campylobacter jejuni

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