Metagenomic analysis reveals linkages between cecal microbiota and feed efficiency in Xiayan chickens
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Du W, Deng J, Yang Z, Zeng L, Yang X
Journal
Poultry science
Year
2020
Keywords:
Xiayan chicken, cecal microbiota, feed efficiency, metagenome sequencing
The cecal microbiota plays a critical role in energy harvest and nutrient digestion, influencing intestinal health and the performance of chickens. Feed efficiency (FE) is essential for improving economic efficiency and saving social resources in chicken production and may be affected by the cecal microbiota. Therefore, to investigate the composition and functional capacity of cecum microbes related to FE in Xiayan chicken, an indigenous breed in Guangxi province, metagenome sequencing was performed on chicken cecal contents. 173 male and 167 female chickens were divided into high and low FE groups according to the residual feed intake. The cecal microbial genome was extracted and sequenced. The results showed that the genera Bacteroides, Prevotella, and Alistipes were the 3 most abundant in each cecal microbiome. The linear discriminant analysis effect size revealed 6 potential biomarkers in male and 14 in female chickens. Notably, the relative abundance of Lactobacillus in the high FE group was higher than that of the low FE group both in the male and female chickens, and the species Limosilactobacillus oris has a higher score in the high FE group of male chickens. In contrast, some potentially pathogenic microorganisms such as Campylobacter avium in females and Helicobacter pullorum in males were enriched in the low FE group. Predictive functional analysis showed that the high FE group in male chickens had a greater ability of xenobiotics biodegradation and metabolism and signaling molecules and interaction. In addition, the host sex was found to exert effects on the cecal microbial composition and function associated with FE. These results increased our understanding of the cecal microbial composition and identified many potential biomarkers related to FE, which may be used to improve the FE of the chickens.
Experiment 1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Gallus gallus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Caecum Blind intestine,Blindgut,Caeca,Caecum,Ceca,Cecum,Intestinum caecum,Intestinum crassum caecum,Intestinum crassum cecum,caecum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Growth condition GrowthCondition,Growth condition,growth condition
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Male Low Feed Efficiency (L-FE) groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Male High Feed Efficiency (H-FE) groups
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Male chickens with the lowest Residual Feed Intake(RFI)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
Signature 1
Source: Figure 2A
Description: Significant differences in the cecum between Low-FE and High-FE groups in male chickens.
Abundance in Group 1: increased abundance in Male High Feed Efficiency (H-FE) groups
| NCBI | Quality Control | Links |
|---|---|---|
| Limosilactobacillus oris | ||
| Barnesiella sp. An22 |
Revision editor(s): Tosin
Signature 2
Source: Figure 2A
Description: Significant differences in the cecum between Low-FE and High-FE groups in male chickens.
Abundance in Group 1: decreased abundance in Male High Feed Efficiency (H-FE) groups
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacter pullorum | ||
| Subdoligranulum variabile | ||
| unclassified Lentisphaerota |
Revision editor(s): Tosin
Experiment 2
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Growth rate measurement Growth rate measurement,growth rate measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Female Low feed efficiency (L-FE) groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Female High Feed efficiency (H-FE) groups
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Female chickens with the lowest Residual Feed Intake (RFI)
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2B
Description: Significant differences in the cecum between Low-FE and High-FE groups in female chickens.
Abundance in Group 1: increased abundance in Female High Feed efficiency (H-FE) groups
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Pseudomonadota |
Revision editor(s): Tosin
Signature 2
Source: Figure 2B
Description: Significant differences in the cecum between Low-FE and High-FE groups in female chickens.
Abundance in Group 1: decreased abundance in Female High Feed efficiency (H-FE) groups
Revision editor(s): Tosin
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