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Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses

Mohd Shaufi, Mohd Asrore, Sieo, Chin Chin, Chong, Chun Wie, Gan, Han Ming and Ho, Yin Wan 2015, Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses, Gut pathogens, vol. 7, pp. 1-12, doi: 10.1186/s13099-015-0051-7.

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Title Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses
Author(s) Mohd Shaufi, Mohd Asrore
Sieo, Chin Chin
Chong, Chun Wie
Gan, Han MingORCID iD for Gan, Han Ming orcid.org/0000-0001-7987-738X
Ho, Yin Wan
Journal name Gut pathogens
Volume number 7
Article ID 4
Start page 1
End page 12
Total pages 12
Publisher BioMed Central
Place of publication London, Eng.
Publication date 2015
ISSN 1757-4749
Keyword(s) 16S rRNA
broiler chicken
gastrointestinal tract
gut microbiota
metagenomics
next-generation sequencing
gastroenterology
hepatology
microbiology
Summary BACKGROUND: Chicken gut microbiota has paramount roles in host performance, health and immunity. Understanding the topological difference in gut microbial community composition is crucial to provide knowledge on the functions of each members of microbiota to the physiological maintenance of the host. The gut microbiota profiling of the chicken was commonly performed previously using culture-dependent and early culture-independent methods which had limited coverage and accuracy. Advances in technology based on next-generation sequencing (NGS), offers unparalleled coverage and depth in determining microbial gut dynamics. Thus, the aim of this study was to investigate the ileal and caecal microbiota development as chicken aged, which is important for future effective gut modulation.

MATERIAL AND METHODS: Ileal and caecal contents of broiler chicken were extracted from 7, 14, 21 and 42-day old chicken. Genomic DNA was then extracted and amplified based on V3 hyper-variable region of 16S rRNA. Bioinformatics, ecological and statistical analyses such as Principal Coordinate Analysis (PCoA) was performed in mothur software and plotted using PRIMER 6. Additional analyses for predicted metagenomes were performed through PICRUSt and STAMP software package based on Greengenes databases.

RESULTS: A distinctive difference in bacterial communities was observed between ilea and caeca as the chicken aged (P < 0.001). The microbial communities in the caeca were more diverse in comparison to the ilea communities. The potentially pathogenic bacteria such as Clostridium were elevated as the chicken aged and the population of beneficial microbe such as Lactobacillus was low at all intervals. On the other hand, based on predicted metagenomes analysed, clear distinction in functions and roles of gut microbiota such as gene pathways related to nutrient absorption (e.g. sugar and amino acid metabolism), and bacterial proliferation and colonization (e.g. bacterial motility proteins, two-component system and bacterial secretion system) were observed between ilea and caeca, respectively (P < 0.05).

CONCLUSIONS: The caeca microbial communities were more diverse in comparison to ilea. The main functional differences between the two sites were found to be related to nutrient absorption and bacterial colonization. Based on the composition of the microbial community, future gut modulation with beneficial bacteria such as probiotics may benefit the host.
Language eng
DOI 10.1186/s13099-015-0051-7
Field of Research 060503 Microbial Genetics
060408 Genomics
060899 Zoology not elsewhere classified
HERDC Research category C1.1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2015, Mohd Shaufi et al.
Free to Read? Yes
Use Rights Creative Commons Attribution licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30101914

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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.