Longitudinal study across SARS-CoV-2 variants identifies transcriptionally active microbes (TAMs) associated with Delta severity

Devi, Priti; Kumari, Pallawi; Yadav, Aanchal; Tarai, Bansidhar; Budhiraja, Sandeep; Shamim, Uzma; Pandey, Rajesh

doi:10.1016/j.isci.2023.107779

Cited by 5 publications

(1 citation statement)

References 53 publications

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“…In general, all of them have been observed in the microbiota of SARS-CoV-2 infected patients. Moreover, both P. bivia and P. timonensis have been defined as unique microorganisms in COVID-19 patients' microbiota [79,84], whilst M. salivarium, H. parainfluenzae and E. durans were related to a higher abundance and poor outcome in these patients [85][86][87]. Of note, the use of these bacteria as biomarkers of severity in SARS-CoV-2 infection is further supported by the fact that these species exhibited positive correlations with various clinical variables.…”

Section: Discussionmentioning

confidence: 93%

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

Martin-Castaño,

Diez-Echave,

García-García

et al. 2024

Preprint

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Background: Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by severe acute respiratory 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 have been identified yet, maybe due the complex pathogenic mechanisms. The microbiota could play a key role in the infection and in the progression and outcome of the disease. Hence, SARS-CoV-2 infection has been associated with nasopharyngeal and gut dysbiosis and higher abundance of opportunistic pathogens. Methods: To identify new prognostic markers for the disease, a multicenter prospective observational cohort study was carried out in COVID-19 patients that were divided in three cohorts according to their symptomatology: mild (n=24), moderate (n=51) and severe/critical (n=31). Faecal and nasopharyngeal samples were taken and the microbiota was analysed. Results: Microbiota composition could be associated with the severity of the symptoms and the linear discriminant analysis identified the generaMycoplasmaandPrevotellaas severity biomarkers in nasopharyngeal samples, andAllistipes,EnterococcusandEscherichiain faecal samples. Moreover,M. salivariumwas defined as a unique microorganism in COVID-19 patients' nasopharyngeal microbiota whileP. biviaandP. timonensiswere defined in faecal microbiota. A connection between faecal and nasopharyngeal microbiota in COVID-19 patients was also identified as a strong positive correlation betweenP. timonensis(faeces) towardsP. dentalisandM. salivarium(nasopharyngeal) was found in critically ill patients. Conclusions: This ratio could be used as a novel prognostic biomarker for severe COVID-19 patients.

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Section: Discussionmentioning

confidence: 93%

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

Martin-Castaño,

Diez-Echave,

García-García

et al. 2024

Preprint

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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

Yadav,

Devi,

Kumari

et al. 2024

STAR Protocols

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

Yadav,

Kumari,

Devi

et al. 2023

Front. Microbiol.

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

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Longitudinal study across SARS-CoV-2 variants identifies transcriptionally active microbes (TAMs) associated with Delta severity

Cited by 5 publications

References 53 publications

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

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

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

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

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