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A Single-Cell Transcriptomic Atlas of the Ovine Rumen Microbiome Characterizes Lineage-Specific Metabolic Shifts
Sanbao Zhang1, Qinyang Jiang2, Junjie Ma1
1Department of Laboratory Medicine of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China.
Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
|June 15, 2026
Summary
We developed a rapid single-cell RNA sequencing method to map the sheep rumen microbiome. This technique reveals microbial adaptations crucial for host resilience and ecosystem stability under environmental change.
Area of Science:
- Microbial Ecology
- Metagenomics
- Host-Microbiome Interactions
Background:
- Host-associated microbiomes are vital for ecosystem stability and resilience.
- Rumen microbiome analysis is challenging due to complex microbial cell walls hindering transcriptomic profiling.
Purpose of the Study:
- To develop an optimized enzymatic lysis strategy for single-cell transcriptomic profiling of the rumen microbiome.
- To map the sheep rumen microbiome at single-cell resolution and understand its functional organization.
- To investigate microbial responses to host thermal adaptation.
Main Methods:
- Developed a 25-minute time-resolved enzymatic lysis strategy using smRandom-seq.
- Profiled 60,748 cells across 21 sheep rumen samples.
- Applied unsupervised clustering to identify cross-species functional clusters.
Main Results:
- Achieved single-cell resolution, resolving transcriptional states for 213 genera and 662 species.
- Captured previously intractable microbial lineages, including methanogenic archaea.
- Identified seven distinct functional clusters and a spatial coupling between microbial lifestyle and metabolism.
- Linked host resilience to rapid transcriptional activation of energy-metabolism clusters.
- Observed a lineage-specific glycolytic shift in Anaerovibrio lipolyticus contributing to host resilience.
Conclusions:
- Established a foundational resource for rumen microbial ecology.
- Demonstrated a technical framework for dissecting phenotypic plasticity in complex microbiomes.
- Highlighted the role of specific microbial metabolic shifts in host adaptation and resilience.
Keywords:
heat toleranceintra‐species heterogeneitymetabolic shiftrumen microbiomesingle‐cell transcriptomicsMore Related Videos
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