title: Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses.
abstract: 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.
  
  
  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.
authors: Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor Malaysia.
authors: Mohd Asrore
authors: MA
authors: Mohd Shaufi
authors: Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor Malaysia ; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor Malaysia.
authors: Chin Chin
authors: CC
authors: Sieo
authors: Department of Life Sciences, International Medical University, Jalan Jalil Perkasa 19, Taman Esplanade, 57000 Kuala Lumpur, Malaysia.
authors: Chun Wie
authors: CW
authors: Chong
authors: School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia.
authors: Han Ming
authors: HM
authors: Gan
authors: Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor Malaysia.
authors: Yin Wan
authors: YW
authors: Ho
keywords: 16S rRNA; Broiler chicken; Gastrointestinal tract; Gut microbiota; Metagenomics; Next-generation sequencing