The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19

eLife, Год журнала: 2025, Номер 13

Опубликована: Фев. 18, 2025

Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by severe acute syndrome coronavirus 2 (SARS-CoV-2) that displays great variability in clinical phenotype. Many factors have been described to be correlated with its severity, and microbiota could play key role the infection, progression, outcome of disease. SARS-CoV-2 infection has associated nasopharyngeal gut dysbiosis higher abundance opportunistic pathogens. To identify new prognostic markers for disease, multicentre prospective observational cohort study was carried out COVID-19 patients divided into three cohorts based on symptomatology: mild (n = 24), moderate 51), severe/critical 31). Faecal samples were taken, analysed. Linear discriminant analysis identified Mycoplasma salivarium , Prevotella dentalis Haemophilus parainfluenzae as biomarkers microbiota, while bivia timonensis defined faecal microbiota. Additionally, connection between identified, significant ratio P. (faeces) M. (nasopharyngeal) abundances found critically ill patients. This serve novel tool identifying cases.

Язык: Английский

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The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Янв. 13, 2024

ABSTRACT Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by severe acute syndrome coronavirus 2 (SARS-CoV-2) that displays great variability in clinical phenotype. Many factors have been described to be correlated with its severity, and microbiota could play key role the infection, progression, outcome of disease. SARS-CoV-2 infection has associated nasopharyngeal gut dysbiosis higher abundance opportunistic pathogens. To identify new prognostic markers for disease, multicenter prospective observational cohort study was carried out COVID-19 patients divided into three cohorts based on symptomatology: mild (n=24), moderate (n=51), severe/critical (n=31). Faecal samples were taken, analyzed. Linear discriminant analysis identified M. salivarium , P. dentalis H. parainfluenzae as biomarkers microbiota, while bivia timonensis defined faecal microbiota. Additionally, connection between identified, significant ratio (faeces) (nasopharyngeal) abundances found critically ill patients. This serve novel tool identifying cases.

Язык: Английский

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Protocol to decode the role of transcriptionally active microbes in SARS-CoV-2-positive patients using an RNA-seq-based approach

STAR Protocols, Год журнала: 2024, Номер 5(2), С. 103071 - 103071

Опубликована: Май 19, 2024

The elucidation of the role microorganisms in human infections has been hindered by difficulties using conventional culture-based techniques. Here, we present a protocol for investigation transcriptionally active microbes (TAMs) an RNA sequencing (RNA-seq)-based approach. We describe steps isolation, viral genome sequencing, RNA-seq library preparation, and metatranscriptomic transcriptomic analysis. This permits comprehensive evaluation TAMs' contributions to differential severity infectious diseases, with particular focus on diseases such as COVID-19. For complete details use execution this protocol, please refer Devi et al.1

Язык: Английский

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Metatranscriptomic insights into the dengue patient blood microbiome: Enhanced microbial diversity and metabolic activity in severe patients

PLoS neglected tropical diseases, Год журнала: 2024, Номер 18(10), С. e0012589 - e0012589

Опубликована: Окт. 17, 2024

Background Dengue is the most re-emergent infection, with approximately 100 million new cases reported annually, yet no effective treatment or vaccine exists. Here, we aim to define microbial community structure and their functional profiles in dengue positive patients varying disease severity. Methodology/Principal findings Hospital admitted 112 dengue-positive blood samples were analyzed by dual RNA-sequencing simultaneously identify transcriptionally active microbes (TAMs), expressed genes associated pathways. Results highlight that severe exhibited increased diversity presence of opportunistic species (unique core) which includes Bacillus cereus , Burkholderia pseudomallei Streptococcus suis Serratia marcescens . The profile analysis revealed enriched metabolic pathways such as protein degradation, nucleotide biosynthesis, ion transport, cell shape integrity, ATP formation cases, indicating high energy demands adaptability these microbes. Conclusion Our metatranscriptomic approach provides a species-level characterization microbiome composition reveals heightened TAMs dengue, underscoring need for further research into role microbiota progression. Comparing signatures across severity classes early offers unique potential convenient diagnosis infection.

Язык: Английский

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Dual RNA-Seq reveals transcriptionally active microbes (TAMs) dynamics in the serum of dengue patients associated with disease severity

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Ноя. 30, 2023

Introduction Dengue virus (DENV) is a flavivirus that has emerged as global health threat, characterized by either asymptomatic or mild self-limiting febrile illness, but subset of DENV outbreaks have been associated with severe disease. Studies looked into the host immune response and dengue viral load during infection. However, it remains unknown how active microbial isolates modulate In this study, we demonstrate significance in-depth analysis microbiota composition in serum samples dengue-infected patients. Materials methods RNA was extracted from collected 24 positive The human mapped reads generated through RNA-Sequencing (RNA-Seq) were removed, while unmapped (non-human) employed for taxonomic classification using Kraken2 Bracken2. Further, assessed initial blood parameters analyzing complete count (CBC) profile Results Findings revealed differential abundance commensals pathogenic microbes early period hospitalized patients, segregated into, High Viral Reads (HVR) Low (LVR). Campylobacter genus abundant HVR whereas Lactobacillus dominated LVR At species level, exhibited higher unique potential opportunistic microbes, compared to commensal microbes’ enrichment patients’. We hypothesize might alter observed increase preponderance pathogens an absence HVR. presence explain, i) overall lower HVR, ii) shift lymphocytes (high) neutrophils (low) counts; resulting comparatively milder clinical manifestation group. Our findings may help understanding co-infection aspect will be important develop therapeutics vaccines. Discussion This study highlights unexplored roles TAMs modulating disease severity metatranscriptomic sequencing. serves enhance our distinctive hematologic signatures infection stage differentiate patients high those low reads.

Язык: Английский

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The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19

eLife, Год журнала: 2024, Номер unknown

Опубликована: Март 26, 2024

Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by severe acute syndrome coronavirus 2 (SARS-CoV-2) that displays great variability in clinical phenotype. Many factors have been described to be correlated with its severity, and microbiota could play key role the infection, progression, outcome of disease. SARS-CoV-2 infection has associated nasopharyngeal gut dysbiosis higher abundance opportunistic pathogens. To identify new prognostic markers for disease, multicentre prospective observational cohort study was carried out COVID-19 patients divided into three cohorts based on symptomatology: mild (n = 24), moderate 51), severe/critical 31). Faecal samples were taken, analysed. Linear discriminant analysis identified Mycoplasma salivarium, Prevotella dentalis, Haemophilus parainfluenzae as biomarkers microbiota, while bivia timonensis defined faecal microbiota. Additionally, connection between identified, significant ratio P. (faeces) dentalis M. salivarium (nasopharyngeal) abundances found critically ill patients. This serve novel tool identifying cases.

Язык: Английский

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The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19

Опубликована: Март 26, 2024

Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by severe acute syndrome coronavirus 2 (SARS-CoV-2) that displays great variability in clinical phenotype. Many factors have been described to be correlated with its severity but no specific determinants of infection outcome identified yet, maybe due the complex pathogenic mechanisms. The microbiota could play key role and progression disease. Hence, SARS-CoV-2 has associated nasopharyngeal gut dysbiosis higher abundance opportunistic pathogens.To identify new prognostic markers for disease, multicenter prospective observational cohort study was carried out COVID-19 patients were divided three cohorts according their symptomatology: mild (n=24), moderate (n=51) severe/critical (n=31). Faecal samples taken analysed.Microbiota composition symptoms linear discriminant analysis genera Mycoplasma Prevotella as biomarkers samples, Allistipes , Enterococcus Escherichia faecal samples. Moreover, M. salivarium defined unique microorganism patients’ while P. bivia timonensis microbiota. A connection between also strong positive correlation (faeces) towards dentalis (nasopharyngeal) found critically ill patients.This ratio used novel biomarker patients.

Язык: Английский

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Immunocompromised or Inter-individual Variabilities?

Опубликована: Янв. 1, 2024

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Comorbidity, Age and Gender

Опубликована: Янв. 1, 2024

Язык: Английский

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Role of Co-infections in Pathogen Clearance

Опубликована: Янв. 1, 2024

Язык: Английский

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