Comparison of changes in fecal microbiota of calves with and without dam
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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 M, Wang Z, Wang L, Xue B, Hu R, Zou H, Liu S, Shah AM, Peng Q
Journal
PeerJ
Year
2022
Keywords:
Calf, Cultivation method, Dynamics, Microbial community
In pastoral areas and semi-agricultural and semi-pastoral areas of Sichuan, beef cattle breeding mode is mainly dependent on nature to raise livestock. On the one hand, owing to the shortage of forage grass in spring, cows suffer from malnutrition. On the other hand, competition for milk between human and livestock further deepens the malnutrition of newborn calves, and the mortality rate even exceeds 40%, resulting in serious waste of beef cattle source resources. The objective of this study was to investigate the effect of different cultivation methods (calves with and without dam) and age on calves hindgut microbiome. Sixteen healthy calves (Yak ♂ × Pian cattle ♀, with similar birthday 0 ± 2 d and body weight 13.1 ± 1.13 kg), were selected and randomly divided into two groups. The control group was cultivated with heifers, whereas the treatment group was cultivated without heifers and was fed milk replacer during the whole 95 days formal experimental period. Fecal samples were collected on 35, 65 and 95 days of age for high-throughput sequencing. The α-diversity was different between the two groups on day 35; however, the bacterial species richness and diversity was almost not different on day 95. Principal coordinates analysis revealed significant difference between the two groups on all the three time points, and the timepoints of day 65 and 95 were closer and separated from the timepoints of day 35 in calves with dam, whereas the timepoints of day 35 and 65 were closer and separated from day 95 in calves without dam. As time passed, the abundance of Firmicutes increased, while Proteobacteria and Actinobacteria decreased in calves with dam. But in calves without dam, the abundance of Bacteroidetes and Proteobacteria increased on day 65 and then decreased on day 95. In genus level, the relative abundance of Bacteroides decreased in calf with dam while its abundance increased first and then decreased in calf without dam but both resulted in the range of 3.5~4.5%. The relative abundance of Lactobacillus decreased, whereas Ruminococcaceae UCG-005 increased in both groups as the calf grew up. It was concluded that the richness and evenness of the microbial communities was higher in calves with dam than without dam, and a stable gut microbiome in calve with dam is established earlier than calf without dam.
Experiment 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Bos grunniens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breastfeeding duration Breastfeeding duration,breastfeeding duration
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Calves with dam on day 35
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Calves without dam on day 35
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Calves without dam on day 35 of the whole 95 days formal experimental period.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- none
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
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
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24
Source: Figures 5&6
Description: Differentially abundant taxa between calves with dam at day 35 of experiment, and calves without dam at day 35 of experiment.
Abundance in Group 1: increased abundance in Calves without dam on day 35
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Myroides | ||
| Paraeggerthella | ||
| Peptostreptococcus |
Revision editor(s): Folakunmi
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24
Source: Figures 5&6
Description: Differentially abundant taxa between calves with dam at day 35 of experiment, and calves without dam at day 35 of experiment.
Abundance in Group 1: decreased abundance in Calves without dam on day 35
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Escherichia/Shigella sp. | ||
| Parabacteroides |
Revision editor(s): Folakunmi
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-21
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Calves with dam on day 65
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Calves without dam on day 65
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Calves without dam on day 65 of the whole 95 days formal experimental period.
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
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-21
Source: Figures 5&6
Description: Differentially abundant taxa between calves with dam at day 65 of experiment, and calves without dam at day 65 of experiment.
Abundance in Group 1: increased abundance in Calves without dam on day 65
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Lactobacillus | ||
| unclassified Oscillospiraceae |
Revision editor(s): Folakunmi
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-21
Source: Figures 5&6
Description: Differentially abundant taxa between calves with dam at day 65 of experiment, and calves without dam at day 65 of experiment.
Abundance in Group 1: decreased abundance in Calves without dam on day 65
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcaceae bacterium UCG-005 | ||
| Treponema | ||
| Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group | ||
| unclassified Oscillospiraceae |
Revision editor(s): Folakunmi
Experiment 3
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-21
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Calves with dam on day 95
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Calves without dam on day 95
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Calves without dam on day 95 of the whole 95 days formal experimental period.
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
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24
Source: Figures 5&6
Description: Differentially abundant taxa between calves with dam at day 95 of experiment, and calves without dam at day 95 of experiment.
Abundance in Group 1: increased abundance in Calves without dam on day 95
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacterium coprostanoligenes | ||
| Treponema |
Revision editor(s): Folakunmi
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24
Source: Figures 5&6
Description: Differentially abundant taxa between calves with dam at day 95 of experiment, and calves without dam at day 95 of experiment.
Abundance in Group 1: decreased abundance in Calves without dam on day 95
| NCBI | Quality Control | Links |
|---|---|---|
| Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group | ||
| Ruminococcaceae bacterium UCG-005 |
Revision editor(s): Folakunmi
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