ArticleSignal transduction and targeted therapy2023
Metatranscriptome of human lung microbial communities in a cohort of mechanically ventilated COVID-19 Omicron patients.
Article in Signal transduction and targeted therapy, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed, 18 citations in OpenAlex.
- Dynamic balance of the lung microbiome in health and respiratory diseases.Chinese medical journal · 2026Review
- The gut-joint axis in osteoarthritis.Nature reviews. Rheumatology · 2026Review
- Assessing links between dental fluorosis and oral/systemic health via salivary microbiome in Chinese young adults.International dental journal · 2026Article
- Lower airway microbiota compositions and diversity among ventilator-associated pneumonia patients across COVID-19 epidemic phases: a retrospective study.Microbiology spectrum · 2025Article
- Application of targeted metagenomic next-generation sequencing in pneumonia patients.Microbiology spectrum · 2025Article
- Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics.Communications biology · 2025Article
- Integrative single-cell and metagenomic analysis dissects SARS-CoV-2 shedding modes in human respiratory tract.Biosafety and health · 2025Article
- Genetic characterization of the respiratory tract viruses in Jilin, Northeast China, 2023.Frontiers in public health · 2025Article
- Multi-omics decodes host-specific and environmental microbiome interactions in sepsis.Frontiers in microbiology · 2025Review
- Comparison between metatranscriptomics and viral metagenomics, 16S, and host transcriptomics for comprehensive profiling of the respiratory microbiome and host response.Frontiers in microbiology · 2025Article
- Fungal lung disease.The European respiratory journal · 2024Review
- Clinical implications of trichomonads detected in bronchoalveolar fluid by metagenomic next-generation sequencing: a multicenter retrospective study.Frontiers in cellular and infection microbiology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
34 authors at 8 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) infected a substantial proportion of Chinese population, and understanding the factors underlying the severity of the disease and fatality is valuable for future prevention and clinical treatment. We recruited 64 patients with invasive ventilation for COVID-19 and performed metatranscriptomic sequencing to profile host transcriptomic profiles, plus viral, bacterial, and fungal content, as well as virulence factors and examined their relationships to 28-day mortality were examined. In addition, the bronchoalveolar lavage fluid (BALF) samples from invasive ventilated hospital/community-acquired pneumonia patients (HAP/CAP) sampled in 2019 were included for comparison. Genomic analysis revealed that all Omicron strains belong to BA.5 and BF.7 sub-lineages, with no difference in 28-day mortality between them. Compared to HAP/CAP cohort, invasive ventilated COVID-19 patients have distinct host transcriptomic and microbial signatures in the lower respiratory tract; and in the COVID-19 non-survivors, we found significantly lower gene expressions in pathways related viral processes and positive regulation of protein localization to plasma membrane, higher abundance of opportunistic pathogens including bacterial Alloprevotella, Caulobacter, Escherichia-Shigella, Ralstonia and fungal Aspergillus sydowii and Penicillium rubens. Correlational analysis further revealed significant associations between host immune responses and microbial compositions, besides synergy within viral, bacterial, and fungal pathogens. Our study presents the relationships of lower respiratory tract microbiome and transcriptome in invasive ventilated COVID-19 patients, providing the basis for future clinical treatment and reduction of fatality.
Indexed as
Identifiers
What OpenQuestion holds
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.