Metagenomic analysis reveals linkages between cecal microbiota and feed efficiency in Xiayan chickens

Study information

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Reviewed Marked as Reviewed by Svetlana up on 2024-12-13

study design

laboratory experiment

Citation

PMID PubMed identifier for scientific articles.

33248623

DOI Digital object identifier for electronic documents.

10.1016/j.psj.2020.09.076

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

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Curated date: 2024/11/05

Curator: Tosin

Revision editor(s): Tosin

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 (M-LFE) groups

Group 1 name Corresponds to the case (exposed) group for case-control studies

Male High Feed Efficiency (M-HFE) 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

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Curated date: 2024/11/05

Curator: Tosin

Revision editor(s): Tosin

Source: Figure 2A

Description: Significant differences in the cecum between Male Low Feed Efficiency (M-LFE) groups and Male High Feed Efficiency (M-HFE) groups.

Abundance in Group 1: increased abundance in Male High Feed Efficiency (M-HFE) groups

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Barnesiella sp. An22
Limosilactobacillus oris

Revision editor(s): Tosin

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Curated date: 2024/11/05

Curator: Tosin

Revision editor(s): Tosin

Source: Figure 2A

Description: Significant differences in the cecum between Male Low Feed Efficiency (M-LFE) groups and Male High Feed Efficiency (M-HFE) groups.

Abundance in Group 1: decreased abundance in Male High Feed Efficiency (M-HFE) groups

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Helicobacter pullorum
Subdoligranulum variabile
unclassified Lentisphaeria
unclassified Lentisphaerales
unclassified Lentisphaeraceae

Revision editor(s): Tosin

Experiment 2

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Curated date: 2024/11/05

Curator: Tosin

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Female Low feed efficiency (F-LFE) groups

Group 1 name Corresponds to the case (exposed) group for case-control studies

Female High Feed efficiency (F-HFE) 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

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Source: Figure 2B

Description: Significant differences in the cecum between Female Low Feed Efficiency (F-LFE) groups and Female High Feed Efficiency (F-HFE) groups.

Abundance in Group 1: increased abundance in Female High Feed efficiency (F-HFE) groups

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Enterobacteriaceae
Pseudomonadota

Revision editor(s): Tosin

Signature 2

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Source: Figure 2B

Description: Significant differences in the cecum between Female Low Feed Efficiency (F-LFE) groups and Female High Feed Efficiency (F-HFE) groups.

Abundance in Group 1: decreased abundance in Female High Feed efficiency (F-HFE) groups

NCBI	Quality Control	Links
Bacteroidales bacterium WCE2004
Bacteroides sp. CAG:598
Bacteroides togonis
Blautia
Blautia sp. An46
Butyricimonas
Collinsella
Faecalibacterium
Parabacteroides sp. CAG:409
Thomasclavelia
Veillonellales
Campylobacter avium

Revision editor(s): Tosin

Experiment 3

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Curated date: 2024/12/12

Curator: Tosin

Revision editor(s): Tosin

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Male Low Feed Efficiency (M-LFE) groups

Group 1 name Corresponds to the case (exposed) group for case-control studies

Male High Feed Efficiency (M-HFE) 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)

Lab analysis

Statistical Analysis

Statistical test

Kruskall-Wallis

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

Not specified

Signature 1

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Curated date: 2024/12/12

Curator: Tosin

Revision editor(s): Tosin, Aleru Divine

Source: Table 2

Description: Relative abundance of the dominant phyla and genera in the cecum of the high and low feed efficiency (FE) groups of male chickens.

Abundance in Group 1: increased abundance in Male High Feed Efficiency (M-HFE) groups

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Actinomycetota
Alistipes
Bacillota
Lachnoclostridium
Lactobacillus
Megamonas
Parabacteroides
Prevotella
Pseudomonadota
unidentified
Elusimicrobiota

Revision editor(s): Tosin, Aleru Divine

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Reviewed Marked as Reviewed by Svetlana up on 2024-12-13

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Curator: Tosin

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Source: Table 2

Description: Relative abundance of the dominant phyla and genera in the cecum of the high and low feed efficiency (FE) groups of male chickens.

Abundance in Group 1: decreased abundance in Male High Feed Efficiency (M-HFE) groups

NCBI	Quality Control	Links
Bacteroides
Bacteroidota
Blautia
Mediterranea
Methanobacteriota
Muribaculum
Spirochaetota
Synergistota
Verrucomicrobiota
Fusobacteriota

Revision editor(s): Tosin

Experiment 4

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Reviewed Marked as Reviewed by Svetlana up on 2024-12-13

Curated date: 2024/12/13

Curator: Tosin

Revision editor(s): Tosin

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Female Low Feed Efficiency (F-LFE) groups

Group 1 name Corresponds to the case (exposed) group for case-control studies

Female High Feed Efficiency (F-HFE) 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

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Curated date: 2024/12/13

Curator: Tosin

Revision editor(s): Tosin, Aleru Divine

Source: Table 2

Description: Relative abundance of the dominant phyla and genera in the cecum of the high and low feed efficiency (FE) groups of female chickens.

Abundance in Group 1: increased abundance in Female High Feed Efficiency (F-HFE) groups

NCBI	Quality Control	Links
Alistipes
Fusobacteriota
Lactobacillus
Mediterranea
Methanobacteriota
Pseudomonadota
Spirochaetota
Verrucomicrobiota
unidentified

Revision editor(s): Tosin, Aleru Divine

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-12-13

Curated date: 2024/12/13

Curator: Tosin

Revision editor(s): Tosin

Source: Table 2

Description: Relative abundance of the dominant phyla and genera in the cecum of the high and low feed efficiency (FE) groups of female chickens.

Abundance in Group 1: decreased abundance in Female High Feed Efficiency (F-HFE) groups

NCBI	Quality Control	Links
Actinomycetota
Bacillota
Bacteroidota
Synergistota
Elusimicrobiota
Bacteroides
Prevotella
Muribaculum
Megamonas
Blautia
Lachnoclostridium
Parabacteroides

Revision editor(s): Tosin