Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Romani L, Del Chierico F, Pane S, Ristori MV, Pirona I, Guarrasi V, Cotugno N, Bernardi S, Lancella L, Perno CF, Rossi P, Villani A, Campana A, Palma P, Putignani L
Journal
Microbiology spectrum
Year
2024
Keywords:
COVID-19, SARS-CoV-2, children, nasopharyngeal microbiota, respiratory tract
UNLABELLED: The relationship between COVID-19 and nasopharyngeal (NP) microbiota has been investigated mainly in the adult population. We explored the NP profile of children affected by COVID-19, compared to healthy controls (CTRLs). NP swabs of children with COVID-19, collected between March and September 2020, were investigated at the admission (T0), 72 h to 7 days (T1), and at the discharge (T2) of the patients. NP microbiota was analyzed by 16S rRNA targeted-metagenomics. Data from sequencing were investigated by QIIME 2.0 and PICRUSt 2. Multiple machine learning (ML) models were exploited to classify patients compared to CTRLs. The NP microbiota of COVID-19 patients (N = 71) was characterized by reduction of α-diversity compared to CTRLs (N = 59). The NP microbiota of COVID-19 cohort appeared significantly enriched in Streptococcus, Haemophilus, Staphylococcus, Veillonella, Enterococcus, Neisseria, Moraxella, Enterobacteriaceae, Gemella, Bacillus, and reduced in Faecalibacterium, Akkermansia, Blautia, Bifidobacterium, Ruminococcus, and Bacteroides, compared to CTRLs (FDR < 0.001). Exploiting ML models, Enterococcus, Pseudomonas, Streptococcus, Capnocytopagha, Tepidiphilus, Porphyromonas, Staphylococcus, and Veillonella resulted as NP microbiota biomarkers, in COVID-19 patients. No statistically significant differences were found comparing the NP microbiota profile of COVID-19 patients during the time-points or grouping patients on the basis of high, medium, and low viral load (VL). This evidence provides specific pathobiont signatures of the NP microbiota in pediatric COVID-19 patients, and the reduction of anaerobic protective commensals. Our data suggest that the NP microbiota may have a specific disease-related signature since infection onset without changes during disease progression, regardless of the SARS-CoV-2 VL. IMPORTANCE: Since the beginning of pandemic, we know that children are less susceptible to severe COVID-19 disease. A potential role of the nasopharyngeal (NP) microbiota has been hypothesized but to date, most of the studies have been focused on adults. We studied the NP microbiota modifications in children affected by SARS-CoV-2 infection showing a specific NP microbiome profile, mainly composed by pathobionts and almost missing protective anaerobic commensals. Moreover, in our study, specific microbial signatures appear since the first days of infection independently from SARS-CoV-2 viral load.
Experiment 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-4-8
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Nasopharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- COVID-19 2019 novel coronavirus,2019 novel coronavirus infection,2019-nCoV,2019-nCoV infection,beta-CoV,beta-CoVs,betacoronavirus,coronavirus disease 2019,SARS-coronavirus 2,SARS-CoV-2,severe acute respiratory syndrome coronavirus 2,severe acute respiratory syndrome coronavirus 2 infectious disease,β-coronavirus,β-CoV,β-CoVs,COVID-19,cOVID-19
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COVID-19 patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children whose Nasopharyngeal swab were positive for SARS-CoV-2 infection, as assayed by a molecular test.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 59
- Group 1 sample size Number of subjects in the case (exposed) group
- 71
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- none
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-5-6
Source: Figure 3
Description: Differences in bacterial taxa abundance of nasopharyngeal (NP) microbiota in COVID-19 patients VS Control (CTRL) groups
Abundance in Group 1: increased abundance in COVID-19 patients
Revision editor(s): Ndruscilla, Ayibatari, Joan Chuks
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-5-6
Source: Figure 3
Description: Differences in bacterial taxa abundance of nasopharyngeal (NP) microbiota in COVID-19 patients Vs Control (CTRL) groups
Abundance in Group 1: decreased abundance in COVID-19 patients
Revision editor(s): Ndruscilla, Ayibatari, Joan Chuks
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-5-6
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- NO COVID-19 (Patients with diagnosis different from COVID-19)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-5-6
Source: Figure S4
Description: Differences in bacterial taxa abundance of nasopharyngeal (NP) microbiota in COVID-19 patients Vs NO COVID-19 (Patients with diagnosis different from COVID-19)
Abundance in Group 1: increased abundance in COVID-19 patients
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister |
Revision editor(s): Joan Chuks
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-5-6
Source: Figure S4
Description: Differences in bacterial taxa abundance of nasopharyngeal (NP) microbiota in COVID-19 patients Vs NO COVID-19 (Patients with diagnosis different from COVID-19)
Abundance in Group 1: decreased abundance in COVID-19 patients
Revision editor(s): Joan Chuks, ChiomaBlessing
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