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

Aaron McKenna, View ORCID ProfileUmer Zeeshan Ijaz, Carmel Kelly, Mark Linton, View ORCID ProfileWilliam T. Sloan, Brian D. Green, Ursula Lavery, View ORCID ProfileNick Dorrell, View ORCID ProfileBrendan W. Wren, Anne Richmond, View ORCID ProfileNicolae Corcionivoschi, View ORCID ProfileOzan Gundogdu
doi: https://doi.org/10.1101/2020.05.10.084251
Aaron McKenna
1Moy Park, 39 Seagoe Industrial Estate, Portadown, Craigavon, Co. Armagh, BT63 5QE, UK
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Umer Zeeshan Ijaz
2School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
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Carmel Kelly
3Agri-Food and Biosciences Institute, Food Microbiology, Newforge Lane, Belfast, BT9 5PX, UK
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Mark Linton
3Agri-Food and Biosciences Institute, Food Microbiology, Newforge Lane, Belfast, BT9 5PX, UK
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William T. Sloan
2School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
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Brian D. Green
4Institute for Global Food Security, Queen’s University Belfast, University Rd, Belfast BT7 1NN, UK
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Ursula Lavery
1Moy Park, 39 Seagoe Industrial Estate, Portadown, Craigavon, Co. Armagh, BT63 5QE, UK
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Nick Dorrell
5Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
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Brendan W. Wren
5Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
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Anne Richmond
1Moy Park, 39 Seagoe Industrial Estate, Portadown, Craigavon, Co. Armagh, BT63 5QE, UK
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Nicolae Corcionivoschi
3Agri-Food and Biosciences Institute, Food Microbiology, Newforge Lane, Belfast, BT9 5PX, UK
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  • For correspondence: ozan.gundogdu@lshtm.ac.uk Nicolae.Corcionivoschi@afbini.gov.uk
Ozan Gundogdu
5Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
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  • For correspondence: ozan.gundogdu@lshtm.ac.uk Nicolae.Corcionivoschi@afbini.gov.uk
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Abstract

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 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.

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, 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.

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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Competing Interest Statement

AM, AR and UL are employed by company Moy Park. AM is also a PhD student between Moy Park and AFBI. All other authors declare no competing interests.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted May 11, 2020.
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Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter
Aaron McKenna, Umer Zeeshan Ijaz, Carmel Kelly, Mark Linton, William T. Sloan, Brian D. Green, Ursula Lavery, Nick Dorrell, Brendan W. Wren, Anne Richmond, Nicolae Corcionivoschi, Ozan Gundogdu
bioRxiv 2020.05.10.084251; doi: https://doi.org/10.1101/2020.05.10.084251
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Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter
Aaron McKenna, Umer Zeeshan Ijaz, Carmel Kelly, Mark Linton, William T. Sloan, Brian D. Green, Ursula Lavery, Nick Dorrell, Brendan W. Wren, Anne Richmond, Nicolae Corcionivoschi, Ozan Gundogdu
bioRxiv 2020.05.10.084251; doi: https://doi.org/10.1101/2020.05.10.084251

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