No rumen fermentation profiles and associated microbial diversities difference were found between Hu sheep and Karakul sheep fed a cottonseed hull diet

Study information

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Reviewed Marked as Reviewed by Svetlana up on 2025-3-21

study design

laboratory experiment

Citation

PMID PubMed identifier for scientific articles.

39856736

DOI Digital object identifier for electronic documents.

10.1186/s40168-024-02020-7

URI

Authors

Wang J, E G, Zhang M, Zhang Y, Bai T, Pu X, Liu J, Guo X, Sarker S, Cheng L

Journal

Microbiome

Year

2025

Keywords:

Dynamic changes, Hu sheep, Karakul sheep, Rumen bacteria, Rumen metabolome

BACKGROUND: This research aimed to investigate differences in rumen fermentation characteristics between Karakul sheep and Hu sheep reared under identical conditions. The test subjects included newborn Hu and Karakul sheep, which were monitored across three stages: stage I (Weaning period: 15 ~ 30 days), stage II (Supplementary feeding period: 31 ~ 90 days), and stage III (Complete feeding period: 91 ~ 150 days). During the supplementary feeding period, cottonseed hulls were the main roughage source. To analyze the dynamics of rumen fermentation, 16S rRNA sequencing and metabolomics methods were employed, alongside measurements of rumen fermentation parameters and cellulase activity. This comprehensive approach aimed to investigate the potential impact of breed on rumen fermentation indicators, microbial community structure, and metabolites in Hu and Karakul sheep. RESULTS: The 16S rRNA sequencing analysis revealed no significant differences in the relative abundance or dominant bacterial communities in the rumen across all stages. In stage II, rumen bacteria in both Hu and Karakul sheep were relatively stable. However, the Simpson index of Hu sheep in stage II was substantially greater than that of Karakul sheep, demonstrating similarities in the rumen microbial structure between stages II and III. Dynamic variations in fermentation parameters and cellulase activity in the rumen revealed that the indicators in both sheep breeds stabilized at 150 days. Metabolomic results revealed that the metabolic pathways in stage I were mainly concentrated in purine metabolism and lipid metabolism, while stage II was dominated by amino acid metabolism. Stage III involved mainly in pyrimidine and purine metabolism. An exploration of the relationships among rumen microbial biomarkers, key differentially abundant metabolites and rumen characteristics indicated that Karakul sheep exhibited superior lipid metabolism compared to Hu sheep. CONCLUSION: These findings reveal that there were no interbreed differences in the rumen characteristics of Hu and Karakul sheep when fed the same cottonseed hull diet, despite differences in their metabolic pathways. The findings also indicate that the first 20 days represent the initial stage of rumen bacteria in Hu sheep, followed by a transition phase between 20 and 90 days, and a relatively stable stage from 90 to 150 days. These results provide a scientific basis for further understanding the rumen function of sheep and for optimizing their feeding strategies. Video Abstract.

Experiment 1

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Curated date: 2025/03/17

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.

Ovis aries

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Rumen Paunch,Rumen,rumen

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

IH (Hu sheep in Stage 1)

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

IK (Karakul sheep in Stage 1)

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

The sheep in this group were in the weaning period (15 to 30 days) and they were fed a basic diet composed of lamb pellets (60%) and green hay (40%). On the final day, they were fasted for 24 hours (withholding water for 2 hours).

Group 0 sample size Number of subjects in the control (unexposed) group

18

Group 1 sample size Number of subjects in the case (exposed) group

18

Lab analysis

Sequencing type

16S

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

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

4

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

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Source: Figure 6 A&B

Description: The cladogram and influence distribution histogram of differential bacterial cladogram and influence distribution histogram showing significant differences in rumen bacteria between Hu sheep and Karakul sheep at stage 1.

Abundance in Group 1: increased abundance in IK (Karakul sheep in Stage 1)

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Bacteroidales
Bacteroidia
Bacteroidota

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Source: Figure 6 A&B

Description: The cladogram and influence distribution histogram of differential bacterial cladogram and influence distribution histogram showing significant differences in rumen bacteria between Hu sheep and Karakul sheep at stage 1.

Abundance in Group 1: decreased abundance in IK (Karakul sheep in Stage 1)

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Lachnospiraceae
Lachnospirales

Revision editor(s): Victoria

Experiment 2

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Curated date: 2025/03/19

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Differences from previous experiment shown

Subjects

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

IIH (Hu sheep in Stage 2)

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

IIK (Karakul sheep in Stage 2)

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

The sheep in this group were in the supplementary feeding period (31 to 90 days) and they were fed the supplementary feeding period diet, during this feeding period, cottonseed hulls were the main roughage source. On the final day, they were fasted for 24 hours (withholding water for 2 hours).

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

decreased

Richness Number of species

unchanged

Signature 1

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Curated date: 2025/03/19

Curator: Victoria

Revision editor(s): Victoria

Source: Figure 6 A&B

Description: The cladogram and influence distribution histogram of differential bacterial cladogram and influence distribution histogram showing significant differences in rumen bacteria between Hu sheep and Karakul sheep at stage 2.

Abundance in Group 1: increased abundance in IIK (Karakul sheep in Stage 2)

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Eubacteriales
Quinella
unclassified Selenomonadaceae
bacterium F082

Revision editor(s): Victoria

Signature 2

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Curated date: 2025/03/19

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Source: Figure 6 A&B

Description: The cladogram and influence distribution histogram of differential bacterial cladogram and influence distribution histogram showing significant differences in rumen bacteria between Hu sheep and Karakul sheep at stage 2.

Abundance in Group 1: decreased abundance in IIK (Karakul sheep in Stage 2)

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unclassified Veillonellaceae UCG_001unclassified Veillonellaceae UCG_001
uncultured rumen bacterium
Veillonellaceae UCG_001Veillonellaceae UCG_001
Acidaminococcaceae
Acidaminococcales
Succiniclasticum
Prevotella
Prevotellaceae

Revision editor(s): Victoria

Experiment 3

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Differences from previous experiment shown

Subjects

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

IIIH (Hu sheep in Stage 3)

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

IIIK (Karakul sheep in Stage 3)

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

The sheep in this group were in the complete feeding period (91 to 150 days) and they were fed the supplementary feeding period diet, during this feeding period, cottonseed hulls were the main roughage source. On the final day, they were fasted for 24 hours (withholding water for 2 hours).

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

Richness Number of species

unchanged

Signature 1

EditHistoryDelete

Flag for review

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Reviewed Marked as Reviewed by Svetlana up on 2025-3-21

Curated date: 2025/03/19

Curator: Victoria

Revision editor(s): Victoria

Source: Figure 6 A&B

Description: The cladogram and influence distribution histogram of differential bacterial cladogram and influence distribution histogram showing significant differences in rumen bacteria between Hu sheep and Karakul sheep at stage 3.

Abundance in Group 1: increased abundance in IIIK (Karakul sheep in Stage 3)

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Bacilli
uncultured rumen bacterium
unclassified Fretibacterium

Revision editor(s): Victoria

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2025-3-21

Curated date: 2025/03/19

Curator: Victoria

Revision editor(s): Victoria

Source: Figure 6 A&B

Description: The cladogram and influence distribution histogram of differential bacterial cladogram and influence distribution histogram showing significant differences in rumen bacteria between Hu sheep and Karakul sheep at stage 3.

Abundance in Group 1: decreased abundance in IIIK (Karakul sheep in Stage 3)

NCBI	Quality Control	Links
uncultured rumen bacterium

Revision editor(s): Victoria