Document Type
Article
Publication Date
5-27-2025
Original Citation
Doing G,
Shanbhag P,
Bell I,
Cassidy S,
Motakis E,
Aiken E,
Oh J,
Adams M.
TEAL-Seq: targeted expression analysis sequencing. mSphere. 2025;10(5):e0098424.
Keywords
JGM, SS1, Humans, Staphylococcus aureus, Microbiota, Staphylococcus epidermidis, Gene Expression Profiling, Metagenome, Skin, High-Throughput Nucleotide Sequencing, Metagenomics
JAX Source
mSphere. 2025;10(5):e0098424.
ISSN
2379-5042
PMID
40261045
DOI
https://doi.org/10.1128/msphere.00984-24
Abstract
Metagenome sequencing enables the genetic characterization of complex microbial communities. However, determining the activity of isolates within a commun ity presents several challenges, including the wide range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many sites. To address these limitations, we developed “targeted expression analysis sequencing” or TEAL-seq, enabling sensitive species-specific analyses of gene expression using highly multiplexed custom probe pools. For proof of concept, we targeted about 1,700 core and accessory genes of Staphylococcus aureus and S. epidermidis, two key species of the skin microbiome. Two targeting methods were applied to laboratory cultures and human nasal swab specimens. Both methods showed a high degree of specificity, with >90% reads on target, even in the presence of complex microbial or human background DNA/RNA. Targeting using molecular inversion probes demonstra ted excellent correlation in inferred expression levels with bulk RNA-seq. Furthermore, we show that a linear pre-amplification step to increase the number of nucleic acids for analysis yielded consistent and predictable results when applied to complex samples and enabled profiling of expression from as little as 1 ng of total RNA. TEAL-seq is much less expensive than bulk metatranscriptomic profiling, enables detection across a greater dynamic range, and uses a strategy that is readily configurable for determining the transcriptional status of organisms in any microbial community.
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This work is licensed under a Creative Commons Attribution 4.0 International License.