ArticleGut microbes
A metatranscriptomics strategy for efficient characterization of the microbiome in human tissues with low microbial biomass.
Article in Gut microbes. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 18 citations in OpenAlex.
- Advancing the Deciphering of Host-Microbe Crosstalk with Spatial Omics: A Mini-Review.Current microbiology · 2026Review
- Integrating rumen microbiome and host metabolome to investigate feed conversion ratio across different fattening stages in Hu sheep.Animal bioscience · 2026Article
- Dual-transcriptomic analysis of human nasal transcriptome and microbiome reveals host-bacteria associations in symptomatic respiratory infection.BMC genomics · 2026Article
- Trimethylamine-producing microbe Bacillus megaterium KCTC 3007 promotes antitumor immunity in endometrial cancer via type I interferon response pathways.Microbiome · 2026Article
- Comprehensive 16S rRNA gene sequencing and meta-transcriptomic analyses of the female reproductive tract microbiota: two molecular profiles with different messages.Human reproduction open · 2026Article
- In Situ Laser-Capture Microdissection for Detection of Components of the Hair Follicle and Scalp Microbiome.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Fungi dominate eukaryotic microbial assemblages in hot spring biofilms of East and Southeast Asia.Environmental microbiome · 2025Article
- Survival implications of the age-associated tumor and normal adjacent tissue microbiome among colorectal cancer patients.Gut pathogens · 2025Article
- Functional archetypes in the human gut microbiome reveal metabolic diversity, stability, and influence disease-associated signatures.Microbiome · 2025Article
- Non-canonical Metatranscriptomic analysis of COVID-19 and Dengue reveals an expanded microbial and AMR landscape in COVID-19 mortality patients.PLoS pathogens · 2025Article
- Multiomics Integration Reveals Microbial Gene Interactions Shaping Host Responses in a DSS-Induced Colitis Mouse Model.Journal of microbiology and biotechnology · 2025Article
- Harnessing gut microbiota for colorectal cancer therapy: from clinical insights to therapeutic innovations.NPJ biofilms and microbiomes · 2025Review
- Modulation of Gut Microbiota and Antibiotic Resistance Genes by Heat-KilledBioengineering (Basel, Switzerland) · 2025Article
- Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.Microbiology and molecular biology reviews : MMBR · 2025Review
- Microbiota and gastric cancer: from molecular mechanisms to therapeutic strategies.Frontiers in cellular and infection microbiology · 2025Review
- Review
- Impact of database choice and confidence score on the performance of taxonomic classification using Kraken2.aBIOTECH · 2024Article
- Influence of the gut microbiota on immune cell interactions and cancer treatment.Journal of translational medicine · 2024Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The high background of host RNA poses a major challenge to metatranscriptome analysis of human samples. Hence, metatranscriptomics has been mainly applied to microbe-rich samples, while its application in human tissues with low ratio of microbial to host cells has yet to be explored. Since there is no computational workflow specifically designed for the taxonomic and functional analysis of this type of samples, we propose an effective metatranscriptomics strategy to accurately characterize the microbiome in human tissues with a low ratio of microbial to host content. We experimentally generated synthetic samples with well-characterized bacterial and host cell compositions, and mimicking human samples with high and low microbial loads. These synthetic samples were used for optimizing and establishing the workflow in a controlled setting. Our results show that the integration of the taxonomic analysis of optimized Kraken 2/Bracken with the functional analysis of HUMAnN 3 in samples with low microbial content, enables the accurate identification of a large number of microbial species with a low false-positive rate, while improving the detection of microbial functions. The effectiveness of our metatranscriptomics workflow was demonstrated in synthetic samples, simulated datasets, and most importantly, human gastric tissue specimens, thus providing a proof of concept for its applicability on mucosal tissues of the gastrointestinal tract. The use of an accurate and reliable metatranscriptomics approach for human tissues with low microbial content will expand our understanding of the functional activity of the mucosal microbiome, uncovering critical interactions between the microbiome and the host in health and disease.
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