Community composition of cecal microbiota in commercial yellow broilers with high and low feed efficiencies

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Huang Y, Lv H, Song Y, Sun C, Zhang Z, Chen S
Journal
Poultry science
Year
2021
Keywords:
16S rRNA gene, cecal microbiota, feed conversion ratio, microbial community, yellow broiler
The cecal microbiota plays important roles in host food digestion and nutrient absorption, which may in part affect feed efficiency (FE). To investigate the composition and functional differences of cecal microbiota between high (n = 30) and low (n = 29) feed conversion ratio (FCR; metric for FE) groups, we performed 16S rRNA gene sequencing and predicted the metagenome function using Phylogenetic Investigation of Communities by Reconstruction of Unobserved Species in yellow broilers. The results showed that the 2 groups had the same prominent microbes but with differing abundance. Firmicutes, Bacteroidetes, and Actinobacteria were 3 prominent bacterial phyla in the cecal microbial community. Although there were no differences in microbial diversity, compositional differences related to FCR were found via linear discriminant analysis (LDA) effect size; the genus Bacteroides had a significantly higher abundance (LDA >2) in the high FE (HFE) group than in the low FE group. Furthermore, genus Bacteroides had a negative FCR-associated correlation (P < 0.05). Oscillospira was positively correlated with Bacteroides in both groups, whereas Dorea was negatively correlated with Bacteroides in the HFE group. Predictive functional analysis revealed that metabolic pathways such as "starch and sucrose metabolism," "phenylalanine, tyrosine and tryptophan biosynthesis," and "carbohydrate metabolism" were significantly enriched in the HFE group. The relatively subtle differences in FE-associated cecal microbiota composition suggest a possible link between cecal microbiota and FE. Moreover, Bacteroides may potentially be used as biomarkers for FE to improve growth performance in yellow broilers.

Experiment 1


Needs review

Curated date: 2024/10/31

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 rate measurement Growth rate measurement,growth rate measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low feed efficiency (LFE)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High feed efficiency (HFE)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Yellow broilers with low feed conversion ratio (FCR).
Group 0 sample size Number of subjects in the control (unexposed) group
29
Group 1 sample size Number of subjects in the case (exposed) group
30

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4
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
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
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
2.0

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2024/10/31

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 5

Description: LEfSe results for cecal microbiota of HFE and LFE groups.

Abundance in Group 1: increased abundance in High feed efficiency (HFE)

NCBI Quality ControlLinks
Bacteroidaceae
Bacteroides

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/10/31

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 5

Description: LEfSe results for cecal microbiota of HFE and LFE groups.

Abundance in Group 1: decreased abundance in High feed efficiency (HFE)

NCBI Quality ControlLinks
Oscillospiraceae
Rikenellaceae

Revision editor(s): Aleru Divine