Microbial Succession in Elk Dung

Dec 13, 2025 · 1 min read
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Herbivore dung decomposition forms a dynamic microscale ecosystem where microbes drive nutrient cycling and organic matter turnover. We investigated microbial succession during tule elk dung decomposition, focusing on how community shifts relate to changes in carbohydrate-active enzyme (CAZyme) substrate utilization. Using amplicon sequencing and shotgun metagenomics, we tracked temporal changes in community composition, diversity, and functional potential.

Approaches being applied to study microbial communities

Bacterial communities followed a more predictable and directional successional trajectory, while fungal communities were more variable and stochastic. Functional profiles from both metagenome-assembled genomes (MAGs) and amplicon-based proxy proteomes revealed a progression from labile to recalcitrant carbon utilization across decomposition. Substrate-specific CAZyme profiles showed complementary bacterial and fungal roles: bacteria were enriched in enzymes targeting sucrose, starch, and xylan, whereas fungi specialized in degrading cellulose and lignin.

Diversity assays
Substrate utilization potentials in each time point

Metagenomics Microbiome
Cheng-Hung Tsai
Authors
Cheng-Hung Tsai (he/him)
I am a Bioinformatician with a PhD from UC Riverside (Dr. Jason Stajich Lab), specializing in the intersection of software development and large-scale genomics. My work focuses on building efficient UNIX/Python tools for genomics and metagenomics applications. I bring a unique perspective to the dry lab, having spent my early career at the bench mastering protein purification and molecular biology. I am passionate about creating user-friendly, scalable tools that empower researchers to turn raw sequencing data into biological discovery.