Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age
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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
Li A, Yang Y, Qin S, Lv S, Jin T, Li K, Han Z, Li Y
Journal
Microbial cell factories
Year
2021
Keywords:
Age, Gut microbiota, Milk replacer, Weaned, Yimeng black goats
BACKGROUND: Colonization of intestinal microbiota in ruminant during the early life is important to host health, metabolism and immunity. Accumulating evidence revealed the ameliorative effect of milk replacer administration in the gut microbial development of early-weaned ruminants. Yimeng black goats (YBGs) inhabiting Shandong, China show a complex intestinal microbial ecosystem, but studies of their gut microbiota are still insufficient to report. Here, this study was performed to investigate how the gut microbiota develops in weaned YBGs with the effect of age and milk replacer. RESULTS: Results indicated that both age and milk replacer were important factors to change the gut microbiota of YBGs. Although the alpha diversity of gut microbiota did not change with the age of YBGs, the taxonomic compositions significantly changed. The relative abundance of some beneficial bacteria such as Lachnospiraceae, Ruminococcaceae, Ruminiclostridium, Eubacterium and Barnesiella significantly decreased and subsequently increase with age, which contributes to maintain the stability of intestinal environment and realize the diversity of intestinal functions. The relative abundance of Porphyromonas, Brevundimonas, Flavobacterium, Stenotrophomonas, Propionibacterium, Acinetobacter, Enterococcus and Clostridium belong to pathogenic bacteria in milk replacer-treated YBGs was significantly decreased. Additionally, some beneficial bacteria such as Ruminococcus, Ruminococcaceae, Christensenellaceae and Ruminiclostridium also display a trend of decreasing first followed by gradually increasing. CONCLUSIONS: This study first revealed the gut bacterial community alterations in YBGs with the effect of age and milk replacer. This study also characterized the gut microbial distribution in YBGs with different ages and provided better insight into microbial population structure and diversity of YBGs. Moreover, milk replacer may serve as a good applicant for improving gut microbial development in early-weaned YBGs.
Experiment 1
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
- Jejunum Intestinum jejunum,Mid-intestine,Middle intestine,Jejunum,jejunum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Age Age,age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- B-Group (B15.2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- B-Group (B25.2)
- 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 control group (B-Group) whose intestines (Jejunum) were obtained on the 25th 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 6a
Description: The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.
Abundance in Group 1: increased abundance in B-Group (B25.2)
Revision editor(s): Victoria
Signature 2
Source: Figure 6a
Description: The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.
Abundance in Group 1: decreased abundance in B-Group (B25.2)
Revision editor(s): Victoria
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- B-Group (B15.2))
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- B-Group (B45.2)
- 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 control group (B-Group) whose intestines (Jejunum) were obtained on the 45th day of the experiment.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 6b
Description: The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.
Abundance in Group 1: increased abundance in B-Group (B45.2)
| NCBI | Quality Control | Links |
|---|---|---|
| Gaiellales | ||
| Thermoleophilia |
Revision editor(s): Victoria
Signature 2
Source: Figure 6b
Description: The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.
Abundance in Group 1: decreased abundance in B-Group (B45.2)
Revision editor(s): Victoria
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- B-Group (B15.2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- B-Group (B75.2)
- 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 control group (B-Group) whose intestines (Jejunum) were obtained on the 75th day of the experiment.
Lab analysis
Statistical Analysis
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
Signature 1
Source: Figure 6c
Description: The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.
Abundance in Group 1: increased abundance in B-Group (B75.2)
Revision editor(s): Victoria
Signature 2
Source: Figure 6c
Description: The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.
Abundance in Group 1: decreased abundance in B-Group (B75.2)
| NCBI | Quality Control | Links |
|---|---|---|
| Family XIIFamily XII | ||
| Planococcaceae |
Revision editor(s): Victoria
Experiment 4
Differences from previous experiment shown
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- B-Group (B15.4)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- B-Group (B25.4)
- 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 control group (B-Group) whose intestines (Cecum) were obtained on the 25th day of the experiment.
Lab analysis
Statistical Analysis
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
Signature 1
Source: Figure 6d
Description: The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.
Abundance in Group 1: increased abundance in B-Group (B25.4)
Revision editor(s): Victoria
Signature 2
Source: Figure 6d
Description: The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.
Abundance in Group 1: decreased abundance in B-Group (B25.4)
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae |
Revision editor(s): Victoria
Experiment 5
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- B-Group (B45.4)
- 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 control group (B-Group) whose intestines (Cecum) were obtained on the 45th day of the experiment.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 6e
Description: The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.
Abundance in Group 1: increased abundance in B-Group (B45.4)
Revision editor(s): Victoria
Signature 2
Source: Figure 6e
Description: The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.
Abundance in Group 1: decreased abundance in B-Group (B45.4)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerolineaceae | ||
| Anaerolineales | ||
| Anaerolinea | ||
| Lactobacillaceae | ||
| Streptococcaceae | ||
| Lactobacillales | ||
| Bacilli | ||
| Peptostreptococcaceae | ||
| Neisseriaceae | ||
| Neisseriales |
Revision editor(s): Victoria
Experiment 6
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- B-Group (B75.4)
- 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 control group (B-Group) whose intestines (Cecum) were obtained on the 75th day of the experiment.
Lab analysis
Statistical Analysis
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
Signature 1
Source: Figure 6f
Description: The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.
Abundance in Group 1: increased abundance in B-Group (B75.4)
Revision editor(s): Victoria
Signature 2
Source: Figure 6f
Description: The cladogram obtained from LEfSe analysis shows the different taxa in microbiota of YBGs with different ages.
Abundance in Group 1: decreased abundance in B-Group (B75.4)
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseriaceae | ||
| Neisseriales | ||
| Pasteurellaceae | ||
| Pasteurellales |
Revision editor(s): Victoria
Experiment 7
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Jejunum Intestinum jejunum,Mid-intestine,Middle intestine,Jejunum,jejunum
- 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 (B15.2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- R-Group (R15.2)
- 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 (Jejunum) were obtained on the 15th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Experiment 8
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- B-Group (B25.2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- R-Group (R25.2)
- 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 (Jejunum) were obtained on the 25th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Experiment 9
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- B-Group (B45.2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- R-Group (R45.2)
- 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 (Jejunum) were obtained on the 45th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.
Lab analysis
Statistical Analysis
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
Experiment 10
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- B-Group (B75.2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- R-Group (R75.2)
- 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 (Jejunum) 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.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Experiment 11
Differences from previous experiment shown
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- B-Group (B15.4)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- R-Group (R15.4)
- 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 15th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Experiment 12
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- B-Group (B25.4)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- R-Group (R25.4)
- 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 25th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Experiment 13
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- B-Group (B45.4)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- R-Group (R45.4)
- 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 45th day of the experiment. This group was provided with milk replacer after weaning on the 10th day of the experiment.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Experiment 14
Differences from previous experiment shown
Subjects
- 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.
Lab analysis
Statistical Analysis
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
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