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Deciphering Chicken Gut Microbial Dynamics Based On High-throughput 16S RRNA Metagenomics Analyses

Mohd Asrore Mohd Shaufi, C. C. Sieo, C. Chong, H. Gan, Y. Ho
Published 2015 · Medicine, Biology

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BackgroundChicken 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 methodsIleal 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.ResultsA 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).ConclusionsThe 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.
This paper references
10.1080/00071667208415953
The intestinal flora of the chicken in the period 2 to 6 weeks of age, with particular reference to the anaerobic bacteria.
E. M. Barnes (1972)
10.1128/AEM.27.4.678-687.1974
Isolation, culture characteristics, and identification of anaerobic bacteria from the chicken cecum.
J. P. Salanitro (1974)
10.1128/MMBR.62.2.379-433.1998
Type III Protein Secretion Systems in Bacterial Pathogens of Animals and Plants
C. Hueck (1998)
10.1111/j.1574-6941.2002.tb00978.x
Molecular analysis of bacterial populations in the ileum of broiler chickens and comparison with bacteria in the cecum.
J. Gong (2002)
10.1128/AEM.68.1.124-137.2002
16S rRNA-Based Analysis of Microbiota from the Cecum of Broiler Chickens
Xiang-yun Zhu (2002)
10.1111/J.1574-6968.2002.TB11051.X
Diversity and phylogenetic analysis of bacteria in the mucosa of chicken ceca and comparison with bacteria in the cecal lumen.
J. Gong (2002)
10.1007/s00248-002-2015-y
Spatial and Temporal Variation of the Intestinal Bacterial Community in Commercially Raised Broiler Chickens During Growth
P. Wielen (2002)
10.1128/AEM.68.12.5918-5924.2002
Effects of Dietary Fat Source and Subtherapeutic Levels of Antibiotic on the Bacterial Community in the Ileum of Broiler Chickens at Various Ages
A. Knarreborg (2002)
Effects of dietary fat source and subtherapeutic levels of antibiotic on the bacterial community in the ileum of broiler chickens
A Knarreborg (2002)
10.1128/AEM.69.11.6816-6824.2003
Diversity and Succession of the Intestinal Bacterial Community of the Maturing Broiler Chicken
J. Lu (2003)
10.1111/j.1365-2958.2004.04323.x
Identification of host‐specific colonization factors of Salmonella enterica serovar Typhimurium
E. Morgan (2004)
10.1079/WPS200415
Characteristics of the gastrointestinal microbial communities, with special reference to the chicken
J. Apajalahti (2004)
10.1093/JN/134.2.465
Molecular ecological analysis of the gastrointestinal microbiota: a review.
E. Zoetendal (2004)
10.1093/PS/83.7.1093
Microflora ecology of the chicken intestine using 16S ribosomal DNA primers.
E. Amit-Romach (2004)
J Nutr
(2004)
10.1128/IAI.73.4.2344-2350.2005
Identification and Functional Characterization of Chicken Toll-Like Receptor 5 Reveals a Fundamental Role in the Biology of Infection with Salmonella enterica Serovar Typhimurium
Muhammad Iqbal (2005)
10.1099/IJS.0.64517-0
Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum.
Phạm Thị Ngọc Lan (2006)
10.1093/PS/85.7.1151
Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques.
L. Bjerrum (2006)
10.1093/nar/gkl889
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
J. Cole (2007)
10.1111/J.1574-6941.2006.00193.X
16S rRNA gene-based analysis of mucosa-associated bacterial community and phylogeny in the chicken gastrointestinal tracts: from crops to ceca.
J. Gong (2007)
10.1080/17450390701556817
Indigenous bacteria and bacterial metabolic products in the gastrointestinal tract of broiler chickens
H. Rehman (2007)
10.1128/AEM.00062-07
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Q. Wang (2007)
10.1016/J.MIMET.2007.02.005
A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria.
S. Chakravorty (2007)
PRIMER-6. 6.1. In: Book PRIMER-6
K Clarke (2007)
PRIMER-6. 6.1
K Clarke (2007)
10.1371/journal.pone.0002945
Comparative Metagenomics Reveals Host Specific Metavirulomes and Horizontal Gene Transfer Elements in the Chicken Cecum Microbiome
A. Qu (2008)
10.1111/j.1365-2672.2007.03699.x
Effects of zinc bacitracin, bird age and access to range on bacterial microbiota in the ileum and caeca of broiler chickens
J. Gong (2008)
10.1128/AEM.01541-09
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
P. Schloss (2009)
10.1128/AEM.02345-10
Metagenomic Analyses: Past and Future Trends
Carola Simon (2010)
10.1038/ismej.2009.128
Exposure of different bacterial inocula to newborn chicken affects gut microbiota development and ileum gene expression
Y. Yin (2010)
10.1128/JB.00024-10
Growth Phase-Dependent Activation of the DccRS Regulon of Campylobacter jejuni
M. Wösten (2010)
Federation of Animal Science Societies. Guide for the care and use of agricultural animals in research and teaching
(2010)
Guide for the care and use of agricultural animals in research and teaching
(2010)
10.1128/AEM.02772-10
Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads†
Andrea K. Bartram (2011)
10.1128/AEM.02810-10
Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis
P. Schloss (2011)
10.1186/1297-9716-42-82
Colonization factors of Campylobacter jejuni in the chicken gut
D. Hermans (2011)
10.1093/bioinformatics/btr381
UCHIME improves sensitivity and speed of chimera detection
R. Edgar (2011)
10.1371/journal.pone.0027949
Modulations of the Chicken Cecal Microbiome and Metagenome in Response to Anticoccidial and Growth Promoter Treatment
J. Danzeisen (2011)
10.1111/j.1462-2920.2011.02495.x
Key two-component regulatory systems that control biofilm formation in Pseudomonas aeruginosa.
Helga Mikkelsen (2011)
10.1128/AEM.02300-10
Influence of Antimicrobial Feed Additives on Broiler Commensal Posthatch Gut Microbiota Development and Performance
V. Torok (2011)
10.1038/nature09944
Enterotypes of the human gut microbiome
M. Arumugam (2011)
10.1007/s00253-011-3847-5
Intestinal microbiota associated with differential feed conversion efficiency in chickens
Dragana Stanley (2011)
10.3389/fcimb.2012.00025
Host Epithelial Cell Invasion by Campylobacter jejuni: Trigger or Zipper Mechanism?
Tadhg Ó Cróinín (2012)
10.1038/nature11053
Human gut microbiome viewed across age and geography
Tanya Yatsunenko (2012)
10.1111/1469-0691.12023
Microbial culturomics: paradigm shift in the human gut microbiome study.
J. Lagier (2012)
10.1007/s11033-012-1947-7
High through put 16S rRNA gene-based pyrosequencing analysis of the fecal microbiota of high FCR and low FCR broiler growers
K. Singh (2012)
10.1371/journal.pone.0061217
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
P. McMurdie (2013)
10.1093/nar/gks808
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
Anna Klindworth (2013)
10.1038/nbt.2676
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
M. Langille (2013)
10.1371/journal.pone.0060811
Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences
S. Ong (2013)
10.1128/AEM.01043-13
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform
James J Kozich (2013)
10.3382/ps.2012-02822
Bacterial census of poultry intestinal microbiome.
S. Wei (2013)
10.1093/nar/gks1219
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast (2013)
10.1016/j.theriogenology.2012.09.004
Comparative metabolic pathway analysis with special reference to nucleotide metabolism-related genes in chicken primordial germ cells.
D. Rengaraj (2013)
10.3382/ps.2012-02741
Next-generation sequencing: the future of molecular genetics in poultry production and food safety.
S. Díaz-Sánchez (2013)
10.1371/journal.pone.0084290
Highly Variable Microbiota Development in the Chicken Gastrointestinal Tract
Dragana Stanley (2013)
10.1007/s00253-014-5646-2
Microbiota of the chicken gastrointestinal tract: influence on health, productivity and disease
Dragana Stanley (2014)
10.1093/bioinformatics/btu494
STAMP: statistical analysis of taxonomic and functional profiles
Donovan H. Parks (2014)
10.3382/ps.2014-03983
The mRNA expression of amino acid transporters, aminopeptidase N, and the di- and tri-peptide transporter PepT1 in the embryo of the domesticated chicken (Gallus gallus) shows developmental regulation.
K. Miska (2014)
10.1186/1757-4749-6-18
The interplay between Campylobacter and Helicobacter species and other gastrointestinal microbiota of commercial broiler chickens
N. Kaakoush (2014)



This paper is referenced by
10.1093/femsle/fnab058
Avian leukosis virus subgroup J infection alters viral composition in the chicken gut.
Yuan Chen (2021)
10.3390/ani11072065
Absence of Circadian Rhythm in Fecal Microbiota of Laying Hens under Common Light
Yu Zhang (2021)
10.3389/fvets.2021.712226
The Spatial and Temporal Characterization of Gut Microbiota in Broilers
Qianqian Zhou (2021)
10.3390/ani11071941
A Review of the Effects and Production of Spore-Forming Probiotics for Poultry
I. Popov (2021)
10.1016/j.psj.2021.01.019
Community composition of cecal microbiota in commercial yellow broilers with high and low feed efficiencies
Yun Huang (2021)
10.14393/VTN-V27N2-2021-57951
EFFECT OF PHOTOPERIOD ON INTESTINAL MICROBIOTA AND CIRCADIAN RHYTHM, AND ITS INFLUENCE ON PERFORMANCE, THE IMMUNE SYSTEM AND THE WELFARE OF BROILER CHICKENS
Bauer Oliveira e Alvarenga (2021)
10.3390/antibiotics10020146
16S rRNA Sequencing Analysis of the Gut Microbiota in Broiler Chickens Prophylactically Administered with Antimicrobial Agents
M. Cuccato (2021)
10.3389/fmicb.2021.739577
Effects of Subchronic Copper Poisoning on Cecal Histology and Its Microflora in Chickens
Cheng Huang (2021)
10.34101/ACTAAGRAR/1/8455
effect of diet composition, a probiotic and a symbiotic treatment on the ileal microbiota composition of one-week-old broiler chickens
N. Such (2021)
10.3390/ani11030615
Assessment of Microbiota Modulation in Poultry to Combat Infectious Diseases
L. Montoro-Dasi (2021)
10.1016/j.psj.2021.101021
An altered gut microbiota in duck-origin parvovirus infection on cherry valley ducklings is associated with mucosal barrier dysfunction
Q. Luo (2021)
10.3390/biom11070999
Multiomic Approach to Analyze Infant Gut Microbiota: Experimental and Analytical Method Optimization
H. Torrell (2021)
10.1128/mSystems.00729-21
Horizontal Gene Transfer Is the Main Driver of Antimicrobial Resistance in Broiler Chicks Infected with Salmonella enterica Serovar Heidelberg
A. Oladeinde (2021)
10.1128/mSystems.01124-20
Nutraceuticals Induced Changes in the Broiler Gastrointestinal Tract Microbiota
Emese Tolnai (2021)
10.3389/fmicb.2021.726923
Genome-Resolved Metagenomics of the Chicken Gut Microbiome
M. Segura-Wang (2021)
10.1051/parasite/2021047
Understanding the interactions between Eimeria infection and gut microbiota, towards the control of chicken coccidiosis: a review
Thabile Madlala (2021)
10.1371/journal.pone.0244724
Geography as non-genetic modulation factor of chicken cecal microbiota
N. P. Pin Viso (2021)
10.1016/j.psj.2020.12.032
Dietary supplementation with Bacillus subtilis promotes growth performance of broilers by altering the dominant microbial community
Shan Zhang (2021)
10.3390/ani11030840
Microbial Diversity and Community Variation in the Intestines of Layer Chickens
Sha-Sha Xiao (2021)
10.1016/j.psj.2020.09.091
Effect of supplementation of a dairy-originated probiotic bacterium, Propionibacterium freudenreichii subsp. freudenreichii, on the cecal microbiome of turkeys challenged with multidrug-resistant Salmonella Heidelberg1
D. Nair (2021)
10.7717/peerj.10571
Bacterial meta-analysis of chicken cecal microbiota
Luis Alberto Chica Cardenas (2021)
10.3389/fmicb.2021.697553
Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach
A. Boukerb (2021)
10.33073/pjm-2021-001
Effects of Different Ambient Temperatures on Caecal Microbial Composition in Broilers
Yuting Yang (2021)
10.3389/fnut.2021.673316
Effect of Dietary Supplementation With Mixed Organic Acids on Immune Function, Antioxidative Characteristics, Digestive Enzymes Activity, and Intestinal Health in Broiler Chickens
Jiayu Ma (2021)
10.1371/journal.pone.0250075
Gut microbiota of endangered crested ibis: Establishment, diversity, and association with reproductive output
Jian Ran (2021)
10.1038/s41598-020-69928-6
Cecal motility and the impact of Lactobacillus in feather pecking laying hens
N. van Staaveren (2020)
10.1038/s41598-020-69010-1
Bamboo leaf flavone changed the community of cecum microbiota and improved the immune function in broilers
Gang Shu (2020)
10.1016/j.psj.2020.12.023
The effects of dietary supplementation with lotus leaf extract on the immune response and intestinal microbiota composition of broiler chickens
Lei Cheng (2020)
10.36899/japs.2020.3.0061
ENZYMATIC TREATMENT OF PALM KERNEL CAKE IMPROVES INTESTINAL HEALTH, GUT MICROBIOTA AND IMMUNE SYSTEM OF BROILERS
H. A. Aguzey (2020)
10.3390/ani10030391
Diversity of Intestinal Bacterial Microbiota of Indigenous and Commercial Strains of Chickens Using 16S rDNA-Based Analysis
W. Al-Marzooqi (2020)
10.1038/s41598-020-60304-y
Tendentious effects of automated and manual metagenomic DNA purification protocols on broiler gut microbiome taxonomic profiling
Gábor Fidler (2020)
10.1186/s12866-020-01918-0
Changes in the vaginal microbiota associated with primary ovarian failure
Juan-juan Wang (2020)
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