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Comparative analysis of chicken cecal microbial diversity and taxonomic composition in response to dietary variation using 16S rRNA amplicon sequencing

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Abstract

Background

Antibiotic resistance poses a grave threat to One-Health. By replacing antibiotics with non-antibiotic additives (are alternatives to antibiotics, ATAs) like phytogenic feed additives and organic acids in poultry feed. ATAs are a potential alternative as these decline the proliferation of pathogenic bacteria and strengthen gut function in broiler chickens. In this study, we use 16S rRNA amplicon sequencing of the V3-V4 region to evaluate phytogenic feed additives and organic acids on the cecal microbial diversity of broiler chickens.

Methods and results

Two hundred & forty broiler chicks were divided into five treatments comprising: a controlled basal diet (CON), antibiotic group (AB), phytogenic feed additives (PHY), organic acids (ORG), and a combination of PHY + ORG (COM). A distinctive microbial community structure was observed amongst different treatments with increased microbial diversity in AB, ORG, and COM (p < 0.05). The synergistic effects of PHY and ORG increased bacterial population of phyla: Firmicutes, Bacteroides, and Proteobacteria in the cecum. The presence of species, Akkermansia muciniphila (involved in mucin degradation) and Bacillus safensis (a probiotic bacterium) were noticed in COM and PHY, respectively. Clustering analysis revealed a higher relative abundance of similar microbial community composition between AB and ORG groups.

Conclusions

Treatments with PHY and ORG modified the relative abundance and presence/absence of specific microbiota in the chicken cecum. Hence, cecal microbiota modulation through diet is a promising strategy to reduce cross-contamination of zoonotic poultry pathogens, led to healthy and economical broiler meat.

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Data availability

The raw sequence data generated from this study have been submitted to the Sequence Read Archive (SRA) database of the National Center for Biotechnology Information (NCBI) with BioProject accession number PRJNA592164. This article has been submitted to a Research Square (Preprint server) with https://doi.org/10.21203/rs.3.rs-201124/v1. This work is licensed under a Creative Commons Attribution 4.0 International License.

Abbreviations

ACE:

Abundance-based coverage estimator

ATCC:

American type culture collection

bp:

Base pair

EDTA:

Ethylene diamine tetra acetic acid

IBD:

Inflammatory bowel diseases

nt:

Nucleotide

OTUs:

Operational taxonomic units

PCA:

Principal component analysis

PCR:

Polymerase chain reaction

RDP:

Ribosomal database project

s.d.:

Standard deviation

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Acknowledgements

Authors like to acknowledge The Karachi Institute of Biotechnology and Genetic Engineering for their professional support.

Funding

No funding was received for this study.

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Authors and Affiliations

  1. The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Karachi, 75270, Pakistan

    Zubia Rashid, Sitwat Zehra, Abid Azhar & Saddia Galani

  2. KAM School of Life Sciences, Forman Christian College University, Lahore, 54600, Pakistan

    Muhammad Zubair Yousaf

  3. Department of Agriculture and Agribusiness Management, University of Karachi, Karachi, Pakistan

    Syed Muddassar Hussain Gilani

  4. State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China

    Ashaq Ali

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  1. Zubia Rashid
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Contributions

ZR: Conceptualization, Investigation, Methodology, Visualization, Formal analysis, writing-original draft. MZY: Formal analysis, Writing- Review and Editing. SMHG: Investigation, Methodology. SZ: Investigation, Methodology. AA: Formal analysis, Writing- Review and Editing. AA: Supervision, Validation. Saddia Galani: Conceptualization, Supervision, Writing- Review & Editing.

Corresponding author

Correspondence to Saddia Galani.

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Conflict of interest

Authors declare no competing interests.

Ethical approval

This study was approved by The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi ethical review board. The animal trial was conducted under the standard operating procedure of guide for the care and use of agricultural animals in agricultural research and teaching.

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Rashid, Z., Yousaf, M.Z., Gilani, S.M.H. et al. Comparative analysis of chicken cecal microbial diversity and taxonomic composition in response to dietary variation using 16S rRNA amplicon sequencing. Mol Biol Rep 48, 7203–7214 (2021). https://doi.org/10.1007/s11033-021-06712-3

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  • DOI: https://doi.org/10.1007/s11033-021-06712-3

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