Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age/Experiment 14

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Curated date: 2024/05/21

Curator: Victoria

Revision editor(s): Victoria

Subjects

Location of subjects

China

Host species Species from which microbiome was sampled. Contact us to have more species added.

Capra hircus

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

Diet Dietary,Diets,Diet,diet

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

B-Group (B75.4)

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

R-Group (R75.4)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

This group consists of young black goats in the milk replacer group (R Group) whose intestines (Cecum) were obtained on the 75th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.

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

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

V3-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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

increased

Chao1 Abundance-based estimator of species richness

increased

Simpson Estimator of species richness and species evenness: more weight on species evenness

unchanged