The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children

From BugSigDB
Needs review
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


incomplete

Curated date: 2023/10/06

Curator: Karen254.

Revision editor(s): Karen254., Chloe

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 , Oropharyngeal gland , Saliva Nasopharyngeal gland,Gland of oral part of pharynx,Gland of oropharynx,Oral part of pharynx gland,Oropharynx gland,Oropharyngeal gland,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Streptococcus pneumoniae Diplococcus pneumoniae,Micrococcus pneumoniae,Streptococcus pneumoniae
Group 0 name Corresponds to the control (unexposed) group for case-control studies
individuals not colonized with Streptococcus pneumoniae
Group 1 name Corresponds to the case (exposed) group for case-control studies
Colonized with Streptococcus pneumoniae
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
To characterize the dynamics of S. pneumoniae colonization in healthy adults
Group 0 sample size Number of subjects in the control (unexposed) group
62
Group 1 sample size Number of subjects in the case (exposed) group
25
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
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
DNA-DNA Hybridization

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Chi-Square
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
unchanged
Richness Number of species
decreased

Signature 1

incomplete

Curated date: 2023/10/09

Curator: Karen254.

Revision editor(s): Karen254., Chloe

Source: figure 8

Description: Differences between the nasopharyngeal and oropharyngeal microbiota.

Abundance in Group 1: increased abundance in Colonized with Streptococcus pneumoniae

NCBI Quality ControlLinks
Corynebacterium
Dolosigranulum pigrum
Moraxella

Revision editor(s): Karen254., Chloe

Signature 2

incomplete

Curated date: 2023/10/09

Curator: Karen254.

Revision editor(s): Karen254., Chloe

Source: figure 8

Description: Differences between nasopharyngeal and oropharyngeal microbiota

Abundance in Group 1: decreased abundance in Colonized with Streptococcus pneumoniae

NCBI Quality ControlLinks
Leptotrichiaceae
Prevotellaceae
Veillonellaceae

Revision editor(s): Karen254., Chloe