Altered infective competence of the human gut microbiome in COVID-19

Nies, Laura de; Galata, Valentina; Martin-Gallausiaux, Camille; Despotovic, Milena; Busi, Susheel Bhanu; Snoeck, Chantal; Delacour, Lea; Budagavi, Deepthi Poornima; Laczny, Cédric Christian; Habier, Janine; Lupu, Paula-Cristina; Halder, Rashi; Fritz, Joëlle V.; Marques, Tainá M.; Sandt, Estelle; O’Sullivan, Marc Paul; Ghosh, Soumyabrata; Satagopam, Venkata; Krüger, Rejko; Fagherazzi, Guy; Ollert, Markus; Hefeng, Feng Q.; Wilmes, Paul

doi:10.1101/2022.10.20.512999

Cited by 5 publications

(3 citation statements)

References 93 publications

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“…In patients with moderate symptoms, P. veronii was detected in nasopharyngeal samples whereas P. stercorea, B. cellulosilyficus, B. stercoris and P. copri were identified in stool samples. In general, these findings agree with previous studies in COVID-19 patients [81]. Thus, Xu et al found that infected patients showed higher abundance of B. cellulosilyficus [82], whereas B. stercoris and P. copri were associated with ACE2 upregulation and increased proinflammatory cytokine production, respectively, in COVID-19 patients [79,83].…”

Section: Discussionsupporting

confidence: 91%

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: Discussionsupporting

confidence: 91%

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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“…More recently, de Nies et al (2023) applied metagenomics and metatranscriptomics to the stool samples collected from COVID-19 patients and healthy controls and then conducted an integrative analysis with IMP to reveal the effect of the infection on the gut microbiome community and functions. 101 gNOMO. gNOMO is a bioinformatics pipeline specifically designed to process and analyse metagenomics, metatranscriptomics and metaproteomics data in an integrative manner.…”

Section: Integrated Multi-omics Analysis Tools For Microbiome Studiesmentioning

confidence: 99%

Integrated multi-omics analyses of microbial communities: a review of the current state and future directions

Arıkan

Muth

2023

Mol. Omics

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“…Notably, alterations in the microbiota persisted long after recovery from the infection. The analyses conducted by de Nies et al (2023) revealed an enrichment of virulence factors and antimicrobial resistance genes in individuals with COVID-19. Notably, these genes were predominantly associated with bacterial families exhibiting heightened abundance during SARS-CoV-2 infection, specifically Acidaminococcaceae and Erysipelatoclostridiaceae .…”

Section: Introductionmentioning

confidence: 99%

Gut microbiome dynamics and predictive value in hospitalized COVID-19 patients: a comparative analysis of shallow and deep shotgun sequencing

Kopera,

Gromowski,

Wydmański

et al. 2024

Front. Microbiol.

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The COVID-19 pandemic caused by SARS-CoV-2 has led to a wide range of clinical presentations, with respiratory symptoms being common. However, emerging evidence suggests that the gastrointestinal (GI) tract is also affected, with angiotensin-converting enzyme 2, a key receptor for SARS-CoV-2, abundantly expressed in the ileum and colon. The virus has been detected in GI tissues and fecal samples, even in cases with negative results of the reverse transcription polymerase chain reaction in the respiratory tract. GI symptoms have been associated with an increased risk of ICU admission and mortality. The gut microbiome, a complex ecosystem of around 40 trillion bacteria, plays a crucial role in immunological and metabolic pathways. Dysbiosis of the gut microbiota, characterized by a loss of beneficial microbes and decreased microbial diversity, has been observed in COVID-19 patients, potentially contributing to disease severity. We conducted a comprehensive gut microbiome study in 204 hospitalized COVID-19 patients using both shallow and deep shotgun sequencing methods. We aimed to track microbiota composition changes induced by hospitalization, link these alterations to clinical procedures (antibiotics administration) and outcomes (ICU referral, survival), and assess the predictive potential of the gut microbiome for COVID-19 prognosis. Shallow shotgun sequencing was evaluated as a cost-effective diagnostic alternative for clinical settings. Our study demonstrated the diverse effects of various combinations of clinical parameters, microbiome profiles, and patient metadata on the precision of outcome prognostication in patients. It indicates that microbiological data possesses greater reliability in forecasting patient outcomes when contrasted with clinical data or metadata. Furthermore, we established that shallow shotgun sequencing presents a viable and cost-effective diagnostic alternative to deep sequencing within clinical environments.

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Altered infective competence of the human gut microbiome in COVID-19

Cited by 5 publications

References 93 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

Integrated multi-omics analyses of microbial communities: a review of the current state and future directions

Gut microbiome dynamics and predictive value in hospitalized COVID-19 patients: a comparative analysis of shallow and deep shotgun sequencing

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