AI Insight
Researchers developed CAMASE, a standardized workflow for multiplexed amplicon sequencing that bridges the gap between costly shotgun metagenomics and limited single-gene amplicon sequencing. The workflow simultaneously analyzes multiple taxonomic and functional genes related to elemental cycling (carbon, nitrogen, phosphorus, sulfur, and arsenic) from environmental samples. Testing on 25 samples across freshwater, sediment, and soil environments with 11 different gene amplicons demonstrated high technical reproducibility and cost-effective generation of publication-ready compositional data.
Why it matters
This workflow enables researchers to study both microbial community structure and functional potential in a single experiment without the high costs of metagenomics, making it practical to analyze large sample sets from diverse ecosystems. It provides a standardized approach for investigating how microbial communities contribute to biogeochemical cycling across environmental studies.
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⚠️ Preprint – Noch nicht peer-reviewed
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Microbial communities play key roles in the transformation and cycling of elements ranging from required macronutrients to toxic metalloids. Next-generation sequencing has been applied across multiple ecosystems to probe the interplay of microbial community structure and functional potential with respect to elemental cycling. Shotgun metagenomics collects marker gene sequences without amplification and is costly for large numbers of samples and deep coverage. Conversely, amplicon sequencing of taxonomic marker genes, e.g. 16S and 18S rRNA, is cost-effective for large numbers of samples, but provides limited functional insight. A middle ground between the two approaches is needed to analyze community structure and functional potential within a sample while remaining cost-effective with high throughput. To address this need, we developed a standardized workflow for multiplexed amplicon sequencing from sample collection through data analysis for diverse sample types, including freshwater, sediments, and soils, that produces data and publication-ready figures for multiple taxonomic and functional genes for carbon, nitrogen, phosphorus, sulfur, and arsenic cycling for each sample analyzed. The workflow’s utility was shown by analyzing 11 taxonomic and functional gene amplicons sequenced from 25 samples with high technical replicate similarity. The workflow is named CAMASE for Compositional Analysis of Multiplex Amplicon Sequencing Experiments. This proof-of-concept shows that CAMASE economically produces standard amplicon sequencing outputs (ASV/OTU counts and taxonomy, PCA, and relative abundance plots) for hundreds of amplicon by sample combinations and provides specific recommendations for implementation.