ArticleMicrobiology spectrum2022
Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome.
Article in Microbiology spectrum, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 29 citations in OpenAlex.
- Intracellular microbial shifts during COVID-19 infection and longitudinal recovery revealed by single-cell RNA sequencing.iScience · 2026Article
- SARS-CoV-2 lineages and naso-oropharyngeal bacterial communities in COVID-19 reinfection: A study in West Java, Indonesia.Narra J · 2025Article
- Functional dynamics between resident transcriptionally active microbes (TAMs) and host genes underlie Dengue severity.PLoS neglected tropical diseases · 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
- Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon.Microorganisms · 2025Article
- Genomic insights into bacteriophages: a new frontier in AMR detection and phage therapy.Briefings in functional genomics · 2025Review
- Human microbiome in post-acute COVID-19 syndrome (PACS).Current research in microbial sciences · 2025Article
- Characterization of the gut microbiota in patients with SARS-CoV-2 infection during controlled ovarian stimulation.Journal of ovarian research · 2024Article
- Metatranscriptomic insights into the dengue patient blood microbiome: Enhanced microbial diversity and metabolic activity in severe patients.PLoS neglected tropical diseases · 2024Article
- Clinical evaluation of a multiplex droplet digital PCR for pathogen detection in critically ill COVID-19 patients with bloodstream infections.Infection · 2024Article
- Single-cell RNA-Seq reveals intracellular microbial diversity within immune cells during SARS-CoV-2 infection and recovery.iScience · 2023Article
- Longitudinal study across SARS-CoV-2 variants identifies transcriptionally active microbes (TAMs) associated with Delta severity.iScience · 2023Article
- Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + .Scientific reports · 2023Article
- Unravelling the gut-lung axis: insights into microbiome interactions and Traditional Indian Medicine's perspective on optimal health.FEMS microbiology ecology · 2023Review
- Polymyxin Resistance and Heteroresistance Are Common in Clinical Isolates ofMicrobiology spectrum · 2023Article
- Transcriptionally active nasopharyngeal commensals and opportunistic microbial dynamics define mild symptoms in the COVID 19 vaccination breakthroughs.PLoS pathogens · 2023Article
- Microbial communities of the upper respiratory tract in mild and severe COVID-19 patients: a possible link with the disease course.Frontiers in microbiomes · 2023Article
- A cross-sectional study on the nasopharyngeal microbiota of individuals with SARS-CoV-2 infection across three COVID-19 waves in India.Frontiers in microbiology · 2023Article
- Narrative review of application of metagenomic approaches to study the link between oropharyngeal microbiome and infectious diseases.Frontiers in microbiology · 2023Review
- Dual RNA-Seq reveals transcriptionally active microbes (TAMs) dynamics in the serum of dengue patients associated with disease severity.Frontiers in microbiology · 2023Article
Corrections and comments
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Authors and funding
16 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis. This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs. Microbial co-infections are being investigated as one of the crucial factors for exacerbation of disease severity and complications of COVID-19. A key question remains whether early transcriptionally active microbial signature/s in COVID-19 patients can provide a window for future disease severity susceptibility and outcome? Using complementary metagenomics sequencing approaches, respiratory virus oligo panel (RVOP) and Holo-seq, our study highlights the possible functional role of nasopharyngeal early resident transcriptionally active microbes in modulating disease severity, within recovered patients with sub-phenotypes (mild, moderate, severe) and mortality. The integrative analysis combines patients' clinical parameters, SARS-CoV-2 phylogenetic analysis, microbial differential composition, and their functional role. The clinical sub-phenotypes analysis led to the identification of transcriptionally active bacterial species associated with disease severity. We found significant transcript abundance of Achromobacter xylosoxidans and Bacillus cereus in the mortality, Leptotrichia buccalis in the severe, Veillonella parvula in the moderate, and Actinomyces meyeri and
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