McKenna, AaronIjaz, Umer ZeeshanKelly, Carmel A.Linton, W. Mark R.Sloan, William T.Green, Brian D.Lavery, UrsulaDorrell, NickWren, Brendan W.Richmond, AnneCorcionivoschi, NicolaeGundogdu, Ozan2020-11-182020-11-182020-09-09McKenna, A., Ijaz, U. Z., Kelly, C., Linton, M., Sloan, W. T., Green, B. D., Lavery, U., Dorrell, N., Wren, B. W., Richmond, A., Corcionivoschi, N. and Gundogdu, O. (2020) ‘Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter’, Microbiome. Springer Science and Business Media LLC, 8(1). doi: 10.1186/s40168-020-00908-8.2049-2618https://doi.org/10.1186/s40168-020-00908-8Publication history: Accepted - 17 August 2020; Published online - 9 September 2020Background 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.en© The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.ChickenMicrobiomeCampylobacterProduction systemsEnvironmental FilteringPhylogenetic signalCompetitive exclusionDiversityArticle