The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children
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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.
URI
Authors
Paulo AC, Lança J, Almeida ST, Hilty M, Sá-Leão R
Journal
Microbiome
Year
2023
Keywords:
Healthy adults, Microbiota, Nasopharynx, Oropharynx, Streptococcus pneumoniae
BACKGROUND: The microbiota of the upper respiratory tract is increasingly recognized as a gatekeeper of respiratory health. Despite this, the microbiota of healthy adults remains understudied. To address this gap, we investigated the composition of the nasopharyngeal and oropharyngeal microbiota of healthy adults, focusing on the effect of Streptococcus pneumoniae carriage, smoking habits, and contact with children. RESULTS: Differential abundance analysis indicated that the microbiota of the oropharynx was significantly different from that of the nasopharynx (P < 0.001) and highly discriminated by a balance between the classes Negativicutes and Bacilli (AUC of 0.979). Moreover, the oropharynx was associated with a more homogeneous microbiota across individuals, with just two vs. five clusters identified in the nasopharynx. We observed a shift in the nasopharyngeal microbiota of carriers vs. noncarriers with an increased relative abundance of Streptococcus, which summed up to 30% vs. 10% in noncarriers and was not mirrored in the oropharynx. The oropharyngeal microbiota of smokers had a lower diversity than the microbiota of nonsmokers, while no differences were observed in the nasopharyngeal microbiota. In particular, the microbiota of smokers, compared with nonsmokers, was enriched (on average 16-fold) in potential pathogenic taxa involved in periodontal diseases of the genera Bacillus and Burkholderia previously identified in metagenomic studies of cigarettes. The microbiota of adults with contact with children resembled the microbiota of children. Specifically, the nasopharyngeal microbiota of these adults had, on average, an eightfold increase in relative abundance in Streptococcus sp., Moraxella catarrhalis, and Haemophilus influenzae, pathobionts known to colonize the children's upper respiratory tract, and a fourfold decrease in Staphylococcus aureus and Staphylococcus lugdunensis. CONCLUSIONS: Our study showed that, in adults, the presence of S. pneumoniae in the nasopharynx is associated with a shift in the microbiota and dominance of the Streptococcus genus. Furthermore, we observed that smoking habits are associated with an increase in bacterial genera commonly linked to periodontal diseases. Interestingly, our research also revealed that adults who have regular contact with children have a microbiota enriched in pathobionts frequently carried by children. These findings collectively contribute to a deeper understanding of how various factors influence the upper respiratory tract microbiota in adults. Video Abstract.
Experiment 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Subjects
- Location of subjects
- Portugal
- 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
- Nasopharyngeal gland , Saliva Nasopharyngeal gland,nasopharyngeal gland,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Streptococcus pneumoniae Diplococcus pneumoniae,Micrococcus pneumoniae,Streptococcus pneumoniae,streptococcus pneumoniae
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pneumococcal non-carriers.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pneumococcal carriers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals who carry pneumococci in the nasopharynx
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- MGISEQ-2000
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Source: Table S2.
Description: Bacteria (ASV) differentially present in the nasopharyngeal microbiota of pneumococcal carriers and non-carriers.
Abundance in Group 1: increased abundance in Pneumococcal carriers
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus pneumoniae | ||
| Streptococcus pseudopneumoniae | ||
| Streptococcus mitis | ||
| Haemophilus influenzae | ||
| Fusobacterium nucleatum | ||
| Parvimonas micra |
Revision editor(s): Karen254., Chloe, Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Source: Table S2
Description: Bacteria (ASV) differentially present in the nasopharyngeal microbiota of pneumococcal carriers and non-carriers.
Abundance in Group 1: decreased abundance in Pneumococcal carriers
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus parahaemolyticus | ||
| Neisseria sicca | ||
| Anaerococcus | ||
| Staphylococcus lugdunensis | ||
| Hoylesella buccalis |
Revision editor(s): Karen254., Chloe, Peace Sandy
Experiment 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non- smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The nasopharyngeal area of smokers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Source: Table S3
Description: Bacteria (ASV) differentially present in the nasopharyngeal microbiota of smokers and non-smokers.
Abundance in Group 1: increased abundance in Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus | ||
| Prevotella melaninogenica | ||
| Veillonella atypica | ||
| Burkholderia | ||
| Fusobacterium necrophorum |
Revision editor(s): Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Source: Table S3
Description: Bacteria (ASV) differentially present in the nasopharyngeal microbiota of smokers and non-smokers
Abundance in Group 1: decreased abundance in Smokers
Revision editor(s): Peace Sandy
Experiment 3
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No contact with children
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Contact with children
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The nasopharyngeal microbiota of individuals that regular contact with children.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Source: Table S4
Description: Bacteria (ASV) differentially present in the nasopharyngeal microbiota of individuals that have and do not have regular contact with children.
Abundance in Group 1: increased abundance in Contact with children
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus pneumoniae | ||
| Streptococcus mitis | ||
| Moraxella catarrhalis | ||
| Haemophilus influenzae | ||
| Fusobacterium nucleatum |
Revision editor(s): Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Source: Table S4
Description: Bacteria (ASV) differentially present in the nasopharyngeal microbiota of individuals that have and do not have regular contact with children.
Abundance in Group 1: decreased abundance in Contact with children
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus lugdunensis | ||
| Sphingomonas sp. FARSPH | ||
| Dermacoccus nishinomiyaensis |
Revision editor(s): Peace Sandy
Experiment 4
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Oropharyngeal gland , Saliva Gland of oral part of pharynx,Gland of oropharynx,Oral part of pharynx gland,Oropharynx gland,Oropharyngeal gland,oropharyngeal gland,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pneumococcal non-carriers.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pneumococcal carriers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Oropharyngeal microbiota of pneumococcal carriers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Source: Table S5
Description: Bacteria (ASV) differentially present in the oropharyngeal microbiota of pneumococcal carriers and non-carriers.
Abundance in Group 1: increased abundance in Pneumococcal carriers
Revision editor(s): Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Source: Table S5
Description: Bacteria (ASV) differentially present in the oropharyngeal microbiota of pneumococcal carriers and non-carriers.
Abundance in Group 1: decreased abundance in Pneumococcal carriers
| NCBI | Quality Control | Links |
|---|---|---|
| Leptotrichia | ||
| Alloprevotella tannerae | ||
| uncultured bacterium |
Revision editor(s): Peace Sandy
Experiment 5
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non- smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Oropharyngeal microbiota of smokers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Source: Table S6
Description: Bacteria (ASV) differentially present in the oropharyngeal microbiota of smokers and non-smokers.
Abundance in Group 1: increased abundance in Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus | ||
| Streptococcus pneumoniae | ||
| Burkholderia | ||
| Selenomonas sputigena | ||
| Haemophilus paraphrohaemolyticus |
Revision editor(s): Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Source: Table S6
Description: Bacteria (ASV) differentially present in the oropharyngeal microbiota of smokers and non-smokers.
Abundance in Group 1: decreased abundance in Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria | ||
| Haemophilus parahaemolyticus | ||
| Alloprevotella tannerae | ||
| Hoylesella shahii | ||
| Campylobacter showae | ||
| Tannerella | ||
| Treponema | ||
| Lautropia dentalis |
Revision editor(s): Peace Sandy
Experiment 6
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Contact with Children
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Contact with children
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Oropharyngeal microbiota of individuals that have regular contact with children.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Source: Table S7
Description: Bacteria (ASV) differentially present in the oropharyngeal microbiota of individuals that have and do not have regular contact with children.
Abundance in Group 1: increased abundance in Contact with children
Revision editor(s): Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-10
Source: Table S7
Description: Bacteria (ASV) differentially present in the oropharyngeal microbiota of individuals that have and do not have regular contact with children
Abundance in Group 1: decreased abundance in Contact with children
| NCBI | Quality Control | Links |
|---|---|---|
| Porphyromonas gingivalis | ||
| Alloprevotella rava | ||
| Prevotella | ||
| Prevotella melaninogenica | ||
| Neisseria |
Revision editor(s): Peace Sandy
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