Temporal stability and community assembly mechanisms in healthy broiler cecum

Aqsa Ameer; Youqi Cheng; Farrukh Saleem; Uzma; Aaron McKenna; Anne Richmond; Ozan Gundogdu; William T Sloan; Sundus Javed; Umer Zeeshan Ijaz

doi:10.3389/fmicb.2023.1197838

Temporal stability and community assembly mechanisms in healthy broiler cecum

Front Microbiol. 2023 Sep 13:14:1197838. doi: 10.3389/fmicb.2023.1197838. eCollection 2023.

Authors

Aqsa Ameer¹, Youqi Cheng², Farrukh Saleem¹, Uzma², Aaron McKenna³, Anne Richmond³, Ozan Gundogdu⁴, William T Sloan², Sundus Javed¹, Umer Zeeshan Ijaz^{2

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Affiliations

¹ Department of Biosciences, COMSATS University, Islamabad, Pakistan.
² Water and Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, United Kingdom.
³ Moy Park, Armagh, United Kingdom.
⁴ Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
⁵ Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom.
⁶ College of Science and Engineering, University of Galway, Galway, Ireland.

Abstract

In recent years, there has been an unprecedented advancement in in situ analytical approaches that contribute to the mechanistic understanding of microbial communities by explicitly incorporating ecology and studying their assembly. In this study, we have analyzed the temporal profiles of the healthy broiler cecal microbiome from day 3 to day 35 to recover the stable and varying components of microbial communities. During this period, the broilers were fed three different diets chronologically, and therefore, we have recovered signature microbial species that dominate during each dietary regime. Since broilers were raised in multiple pens, we have also parameterized these as an environmental condition to explore microbial niches and their overlap. All of these analyses were performed in view of different parameters such as body weight (BW-mean), feed intake (FI), feed conversion ratio (FCR), and age (days) to link them to a subset of microbes that these parameters have a bearing upon. We found that gut microbial communities exhibited strong and statistically significant specificity for several environmental variables. Through regression models, genera that positively/negatively correlate with the bird's age were identified. Some short-chain fatty acids (SCFAs)-producing bacteria, including Izemoplasmatales, Gastranaerophilales, and Roseburia, have a positive correlation with age. Certain pathogens, such as Escherichia-Shigella, Sporomusa, Campylobacter, and Enterococcus, negatively correlated with the bird's age, which indicated a high disease risk in the initial days. Moreover, the majority of pathways involved in amino acid biosynthesis were also positively correlated with the bird's age. Some probiotic genera associated with improved performance included Oscillospirales; UCG-010, Shuttleworthia, Bifidobacterium, and Butyricicoccaceae; UCG-009. In general, predicted antimicrobial resistance genes (piARGs) contributed at a stable level, but there was a slight increase in abundance when the diet was changed. To the best of the authors' knowledge, this is one of the first studies looking at the stability, complexity, and ecology of natural broiler microbiota development in a temporal setting.

Keywords: 16SrRNA gene sequencing; assembly; broiler; microbiota; stability.