ArticleNPJ biofilms and microbiomes2018
Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities.
Article in NPJ biofilms and microbiomes, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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Who cites it
34 citing papers in PubMed, 61 citations in OpenAlex.
- MinION Sequencing of colorectal cancer tumour microbiomes-A comparison with amplicon-based and RNA-Sequencing.PloS one · 2020Trial
- Fungal ecology in the age of 'omics.The New phytologist · 2026Review
- The Gut Microbiota: An Essential Component in Understanding Pediatric Obesity: A Narrative Review.Nutrients · 2026Review
- Interpreting fungal ecological contributions through taxonomic and functional profiling of metatranscriptomics.IMA fungus · 2026Review
- Assessing the methanogenic activity of microbial communities enriched from a depleted reservoir.FEMS microbiology ecology · 2025Article
- The Next Generation Fecal Microbiota Transplantation: To Transplant Bacteria or Virome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Review
- Exploring microbial diversity in Greenland Ice Sheet supraglacial habitats through culturing-dependent and -independent approaches.FEMS microbiology ecology · 2023Article
- Identification of Bulgarian Sourdough Microbiota by Metagenomic Approach Using Three Commercially Available DNA Extraction Protocols.Food technology and biotechnology · 2023Article
- Core-predominant gut fungus Kazachstania slooffiae promotes intestinal epithelial glycolysis via lysine desuccinylation in pigs.Microbiome · 2023Article
- Seasonal and geographical differences in the ruminal microbial and chloroplast composition of sika deer (Cervus nippon) in Japan.Scientific reports · 2022Article
- Yeasts Inhabiting Extreme Environments and Their Biotechnological Applications.Microorganisms · 2022Review
- Next-generation sequencing: insights to advance clinical investigations of the microbiome.The Journal of clinical investigation · 2022Review
- The potential for mitigation of methane emissions in ruminants through the application of metagenomics, metabolomics, and other -OMICS technologies.Journal of animal science · 2021Review
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- Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce.mSystems · 2021Article
- Monitoring the microbiome for food safety and quality using deep shotgun sequencing.NPJ science of food · 2021Article
- Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification.mSystems · 2021Article
- Microbiome Community Structure and Functional Gene Partitioning in Different Micro-Niches Within a Sporocarp-Forming Fungus.Frontiers in microbiology · 2021Article
- Simple mapping-based quantification of a mock microbial community using total RNA-seq data.PloS one · 2021Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequencing-based microbiome profiling aims at detecting and quantifying individual members of a microbial community in a culture-independent manner. While amplicon-based sequencing (ABS) of bacterial or fungal ribosomal DNA is the most widely used technology due to its low cost, it suffers from PCR amplification biases that hinder accurate representation of microbial population structures. Shotgun metagenomics (SMG) conversely allows unbiased microbiome profiling but requires high sequencing depth. Here we report the development of a meta-total RNA sequencing (MeTRS) method based on shotgun sequencing of total RNA and benchmark it on a human stool sample spiked in with known abundances of bacterial and fungal cells. MeTRS displayed the highest overall sensitivity and linearity for both bacteria and fungi, the greatest reproducibility compared to SMG and ABS, while requiring a ~20-fold lower sequencing depth than SMG. We therefore present MeTRS as a valuable alternative to existing technologies for large-scale profiling of complex microbiomes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.